9N5T | pdb_00009n5t

Mycobacterium smegmatis 70S ribosome with small molecule drug MK-7762

  • Classification: RIBOSOME
  • Organism(s): Mycolicibacterium smegmatis MC2 155
  • Mutation(s): No 

  • Deposited: 2025-02-04 Released: 2025-12-24 
  • Deposition Author(s): Zhu, J.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Mycobacterium smegmatis 70S ribosome with small molecule drug MK-7762

Zhu, J.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L27A [auth 3]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved domain proteinE [auth BB]33Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3F [auth BC]275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4G [auth BD]201Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S5H [auth BE]214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6I [auth BF]96Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0A2U9Q0X2 (Mycolicibacterium smegmatis (strain MKD8))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7J [auth BG]156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S8K [auth BH]132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9L [auth BI]150Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10M [auth BJ]101Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11N [auth BK]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12O [auth BL]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13P [auth BM]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S14Q [auth BN]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S15R [auth BO]89Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16S [auth BP]156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17T [auth BQ]98Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S18U [auth BR]84Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19V [auth BS]93Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20W [auth BT]86Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S2X [auth BV]277Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4CA [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L5DA [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11GA [auth J]142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13HA [auth K]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16KA [auth N]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth O]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18MA [auth P]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for I7FGD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20OA [auth R]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21PA [auth S]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22QA [auth T]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23RA [auth U]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth W]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth X]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28VA [auth Y]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for I7FJ52 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Find proteins for A0QSD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth a]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth b]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L33ZA [auth c]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth d]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth e]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth f]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L31DB [auth g]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent peptideEB [auth s]5Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth A]3,120Mycolicibacterium smegmatis MC2 155
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth B]118Mycolicibacterium smegmatis MC2 155
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Entity ID: 4
MoleculeChains LengthOrganismImage
16S rRNAD [auth BA]1,528Mycolicibacterium smegmatis MC2 155
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Entity ID: 25
MoleculeChains LengthOrganismImage
P/P-site Phe-tRNAY [auth BW]76Mycolicibacterium smegmatis MC2 155
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Entity ID: 26
MoleculeChains LengthOrganismImage
mRNA fragmentZ [auth I]15Mycolicibacterium smegmatis MC2 155
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BWO (Subject of Investigation/LOI)
Query on A1BWO
Download Ideal Coordinates CCD File 
VK [auth A]methyl ({(5S)-3-[4-(1,1-dioxo-1lambda~6~-thiomorpholin-4-yl)-3,5-difluorophenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)carbamate
C16 H19 F2 N3 O6 S
CCYKSCLMFZLAJH-NSHDSACASA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
JO [auth BN]
LO [auth BR]
RO [auth Y]
SO [auth c]
TO [auth f]
JO [auth BN],
LO [auth BR],
RO [auth Y],
SO [auth c],
TO [auth f],
UO [auth g]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth B],
AM [auth BA],
AN [auth BA],
AO [auth BA],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth BA],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth BA],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth BA],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth BA],
EM [auth BA],
EN [auth BA],
EO [auth BA],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
FL [auth BA],
FM [auth BA],
FN [auth BA],
FO [auth BA],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth BA],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HJ [auth A],
HK [auth A],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth BA],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth BM],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JJ [auth A],
JK [auth A],
JL [auth BA],
JM [auth BA],
JN [auth BA],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth BR],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
LL [auth BA],
LM [auth BA],
LN [auth BA],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
ML [auth BA],
MM [auth BA],
MN [auth BA],
MO [auth BW],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
NL [auth BA],
NM [auth BA],
NN [auth BA],
NO [auth C],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth BA],
OM [auth BA],
ON [auth BA],
OO [auth C],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
PL [auth BA],
PM [auth BA],
PN [auth BA],
PO [auth D],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
QL [auth BA],
QM [auth BA],
QN [auth BA],
QO [auth M],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
RL [auth BA],
RM [auth BA],
RN [auth BA],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
SL [auth BA],
SM [auth BA],
SN [auth BA],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
TL [auth BA],
TM [auth BA],
TN [auth BA],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UL [auth BA],
UM [auth BA],
UN [auth BA],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VL [auth BA],
VM [auth BA],
VN [auth BA],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth B],
WL [auth BA],
WM [auth BA],
WN [auth BA],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth B],
XL [auth BA],
XM [auth BA],
XN [auth BA],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth B],
YL [auth BA],
YM [auth BA],
YN [auth BA],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth B],
ZL [auth BA],
ZM [auth BA],
ZN [auth BA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-12-24 
    • Deposition Author(s): Zhu, J.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release