4WF1

Crystal structure of the E. coli ribosome bound to negamycin.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 


Literature

Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.

Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., Prince, D.B., Cate, J.H., Buurman, E.T., Blanchard, S.C.

(2014) Proc Natl Acad Sci U S A 111: 16274-16279

  • DOI: https://doi.org/10.1073/pnas.1414401111
  • Primary Citation of Related Structures:  
    4WF1

  • PubMed Abstract: 

    Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 Å resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.

    • Organizational Affiliation: 

    Discovery Sciences, AstraZeneca R&D Boston, Waltham, MA 02451;


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
CB		218Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Explore P0A7V0 
Go to UniProtKB:  P0A7V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
DB [auth CC]		206Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Explore P0A7V3 
Go to UniProtKB:  P0A7V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
EB [auth CD]		205Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Explore P0A7V8 
Go to UniProtKB:  P0A7V8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
FB [auth CE]		150Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Explore P0A7W1 
Go to UniProtKB:  P0A7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7W1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
GB [auth CF]		100Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
Explore P02358 
Go to UniProtKB:  P02358
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02358
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
HB [auth CG]		151Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02359 (Escherichia coli (strain K12))
Explore P02359 
Go to UniProtKB:  P02359
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02359
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
IB [auth CH]		129Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Explore P0A7W7 
Go to UniProtKB:  P0A7W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7W7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI],
JB [auth CI]		127Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Explore P0A7X3 
Go to UniProtKB:  P0A7X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7X3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ],
KB [auth CJ]		98Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Explore P0A7R5 
Go to UniProtKB:  P0A7R5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
LB [auth CK]		117Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Explore P0A7R9 
Go to UniProtKB:  P0A7R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL],
MB [auth CL]		123Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Explore P0A7S3 
Go to UniProtKB:  P0A7S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7S3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM],
NB [auth CM]		114Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Explore P0A7S9 
Go to UniProtKB:  P0A7S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7S9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN],
OB [auth CN]		100Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12))
Explore P0AG59 
Go to UniProtKB:  P0AG59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG59
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO],
PB [auth CO]		88Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
QB [auth CP]		82Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Explore P0A7T3 
Go to UniProtKB:  P0A7T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ],
RB [auth CQ]		80Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
Explore P0AG63 
Go to UniProtKB:  P0AG63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG63
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR],
SB [auth CR]		55Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Explore P0A7T7 
Go to UniProtKB:  P0A7T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS],
TB [auth CS]		79Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
Go to UniProtKB:  P0A7U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT],
UB [auth CT]		85Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Explore P0A7U7 
Go to UniProtKB:  P0A7U7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU],
VB [auth CU]		51Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
Explore P68679 
Go to UniProtKB:  P68679
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68679
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth BC],
YB [auth DC]		271Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
Explore P60422 
Go to UniProtKB:  P60422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60422
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth BD],
ZB [auth DD]		209Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60438
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AC [auth DE],
Z [auth BE]		201Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
Explore P60723 
Go to UniProtKB:  P60723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60723
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth BF],
BC [auth DF]		177Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P62399 (Escherichia coli (strain K12))
Explore P62399 
Go to UniProtKB:  P62399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62399
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth BG],
CC [auth DG]		176Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
Explore P0AG55 
Go to UniProtKB:  P0AG55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG55
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth BH],
DC [auth DH]		149Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Explore P0A7R1 
Go to UniProtKB:  P0A7R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11DA [auth BI],
EC [auth DI]		141Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Explore P0A7J7 
Go to UniProtKB:  P0A7J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7J7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth BJ],
FC [auth DJ]		142Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
Explore P0AA10 
Go to UniProtKB:  P0AA10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AA10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth BK],
GC [auth DK]		122Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Explore P0ADY3 
Go to UniProtKB:  P0ADY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth BL],
HC [auth DL]		143Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
Explore P02413 
Go to UniProtKB:  P02413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02413
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16HA [auth BM],
IC [auth DM]		136Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Explore P0ADY7 
Go to UniProtKB:  P0ADY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17IA [auth BN],
JC [auth DN]		120Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12))
Explore P0AG44 
Go to UniProtKB:  P0AG44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG44
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18JA [auth BO],
KC [auth DO]		116Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12))
Explore P0C018 
Go to UniProtKB:  P0C018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C018
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19KA [auth BP],
LC [auth DP]		114Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Explore P0A7K6 
Go to UniProtKB:  P0A7K6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7K6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth BQ],
MC [auth DQ]		117Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Explore P0A7L3 
Go to UniProtKB:  P0A7L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth BR],
NC [auth DR]		103Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
Explore P0AG48 
Go to UniProtKB:  P0AG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth BS],
OC [auth DS]		110Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
Explore P61175 
Go to UniProtKB:  P61175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61175
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth BT],
PC [auth DT]		93Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth BU],
QC [auth DU]		102Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60624
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25QA [auth BV],
RC [auth DV]		94Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
Explore P68919 
Go to UniProtKB:  P68919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68919
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth BW],
SC [auth DW]		76Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Explore P0A7L8 
Go to UniProtKB:  P0A7L8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28SA [auth BX],
TC [auth DX]		77Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Explore P0A7M2 
Go to UniProtKB:  P0A7M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29TA [auth BY],
UC [auth DY]		63Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30UA [auth BZ],
VC [auth DZ]		58Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
Explore P0AG51 
Go to UniProtKB:  P0AG51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth B0],
WC [auth D0]		56Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Explore P0A7N4 
Go to UniProtKB:  P0A7N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7N4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33WA [auth B1],
XC [auth D1]		50Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Explore P0A7N9 
Go to UniProtKB:  P0A7N9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7N9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34XA [auth B2],
YC [auth D2]		46Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Explore P0A7P5 
Go to UniProtKB:  P0A7P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7P5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35YA [auth B3],
ZC [auth D3]		64Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Explore P0A7Q1 
Go to UniProtKB:  P0A7Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Q1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36AD [auth D4],
ZA [auth B4]		38Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Explore P0A7Q6 
Go to UniProtKB:  P0A7Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Q6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1AB [auth B5]207Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP7 
Go to UniProtKB:  Q5SLP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLP7
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth AA],
BB [auth CA]		1,539Escherichia coli str. K-12 substr. MG1655
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains LengthOrganismImage
23S rRNAV [auth BA],
WB [auth DA]		2,903Escherichia coli str. K-12 substr. MG1655
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains LengthOrganismImage
5S rRNAW [auth BB],
XB [auth DB]		119Escherichia coli str. K-12 substr. MG1655
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NEG
Query on NEG
Download Ideal Coordinates CCD File 
RP [auth CA]NEGAMYCIN
C9 H20 N4 O4
IKHFJPZQZVMLRH-RNFRBKRXSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IW [auth D4],
MN [auth B4]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth BA]
AH [auth BA]
AI [auth BA]
AE [auth AA],
AF [auth AA],
AG [auth BA],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BA],
AO [auth CA],
AP [auth CA],
AQ [auth DA],
AR [auth DA],
AS [auth DA],
AT [auth DA],
AU [auth DA],
AV [auth DA],
AW [auth DA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth BA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth CA],
BP [auth CA],
BQ [auth DA],
BR [auth DA],
BS [auth DA],
BT [auth DA],
BU [auth DA],
BV [auth DA],
BW [auth DB],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth BA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth CA],
CP [auth CA],
CQ [auth DA],
CR [auth DA],
CS [auth DA],
CT [auth DA],
CU [auth DA],
CV [auth DA],
CW [auth DB],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth BA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth CA],
DP [auth CA],
DQ [auth DA],
DR [auth DA],
DS [auth DA],
DT [auth DA],
DU [auth DA],
DV [auth DA],
DW [auth DB],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth BA],
EO [auth CA],
EP [auth CA],
EQ [auth DA],
ER [auth DA],
ES [auth DA],
ET [auth DA],
EU [auth DA],
EV [auth DA],
EW [auth DL],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth BA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
FN [auth BA],
FO [auth CA],
FP [auth CA],
FQ [auth DA],
FR [auth DA],
FS [auth DA],
FT [auth DA],
FU [auth DA],
FV [auth DA],
FW [auth DL],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth CA],
GP [auth CA],
GQ [auth DA],
GR [auth DA],
GS [auth DA],
GT [auth DA],
GU [auth DA],
GV [auth DA],
GW [auth DQ],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
HN [auth BB],
HO [auth CA],
HP [auth CA],
HQ [auth DA],
HR [auth DA],
HS [auth DA],
HT [auth DA],
HU [auth DA],
HV [auth DA],
HW [auth D2],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
IN [auth BB],
IO [auth CA],
IP [auth CA],
IQ [auth DA],
IR [auth DA],
IS [auth DA],
IT [auth DA],
IU [auth DA],
IV [auth DA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth BA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
JN [auth BB],
JO [auth CA],
JP [auth CA],
JQ [auth DA],
JR [auth DA],
JS [auth DA],
JT [auth DA],
JU [auth DA],
JV [auth DA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth BA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
KN [auth BB],
KO [auth CA],
KP [auth CA],
KQ [auth DA],
KR [auth DA],
KS [auth DA],
KT [auth DA],
KU [auth DA],
KV [auth DA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth BA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
LN [auth BQ],
LO [auth CA],
LP [auth CA],
LQ [auth DA],
LR [auth DA],
LS [auth DA],
LT [auth DA],
LU [auth DA],
LV [auth DA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth BA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
MO [auth CA],
MP [auth CA],
MQ [auth DA],
MR [auth DA],
MS [auth DA],
MT [auth DA],
MU [auth DA],
MV [auth DA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth BA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
NN [auth CA],
NO [auth CA],
NP [auth CA],
NQ [auth DA],
NR [auth DA],
NS [auth DA],
NT [auth DA],
NU [auth DA],
NV [auth DA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth BA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
ON [auth CA],
OO [auth CA],
OP [auth CA],
OQ [auth DA],
OR [auth DA],
OS [auth DA],
OT [auth DA],
OU [auth DA],
OV [auth DA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth BA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
PN [auth CA],
PO [auth CA],
PP [auth CA],
PQ [auth DA],
PR [auth DA],
PS [auth DA],
PT [auth DA],
PU [auth DA],
PV [auth DA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth BA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
QN [auth CA],
QO [auth CA],
QP [auth CA],
QQ [auth DA],
QR [auth DA],
QS [auth DA],
QT [auth DA],
QU [auth DA],
QV [auth DA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth BA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
RN [auth CA],
RO [auth CA],
RQ [auth DA],
RR [auth DA],
RS [auth DA],
RT [auth DA],
RU [auth DA],
RV [auth DA],
SD [auth AA],
SE [auth AA],
SF [auth AA],
SG [auth BA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
SN [auth CA],
SO [auth CA],
SP [auth CT],
SQ [auth DA],
SR [auth DA],
SS [auth DA],
ST [auth DA],
SU [auth DA],
SV [auth DA],
TD [auth AA],
TE [auth AA],
TF [auth AA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
TN [auth CA],
TO [auth CA],
TP [auth DA],
TQ [auth DA],
TR [auth DA],
TS [auth DA],
TT [auth DA],
TU [auth DA],
TV [auth DA],
UD [auth AA],
UE [auth AA],
UF [auth AM],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
UN [auth CA],
UO [auth CA],
UP [auth DA],
UQ [auth DA],
UR [auth DA],
US [auth DA],
UT [auth DA],
UU [auth DA],
UV [auth DA],
VD [auth AA],
VE [auth AA],
VF [auth BA],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
VN [auth CA],
VO [auth CA],
VP [auth DA],
VQ [auth DA],
VR [auth DA],
VS [auth DA],
VT [auth DA],
VU [auth DA],
VV [auth DA],
WD [auth AA],
WE [auth AA],
WF [auth BA],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
WN [auth CA],
WO [auth CA],
WP [auth DA],
WQ [auth DA],
WR [auth DA],
WS [auth DA],
WT [auth DA],
WU [auth DA],
WV [auth DA],
XD [auth AA],
XE [auth AA],
XF [auth BA],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
XN [auth CA],
XO [auth CA],
XP [auth DA],
XQ [auth DA],
XR [auth DA],
XS [auth DA],
XT [auth DA],
XU [auth DA],
XV [auth DA],
YD [auth AA],
YE [auth AA],
YF [auth BA],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
YN [auth CA],
YO [auth CA],
YP [auth DA],
YQ [auth DA],
YR [auth DA],
YS [auth DA],
YT [auth DA],
YU [auth DA],
YV [auth DA],
ZD [auth AA],
ZE [auth AA],
ZF [auth BA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA],
ZN [auth CA],
ZO [auth CA],
ZP [auth DA],
ZQ [auth DA],
ZR [auth DA],
ZS [auth DA],
ZT [auth DA],
ZU [auth DA],
ZV [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.91α = 90
b = 434.31β = 90
c = 624.4γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-10-16
    Changes: Structure summary