9PJ7 | pdb_00009pj7

C. acnes 70S ribosome bound to Doxycycline


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history

Literature

Dual site targeting of the bacterial 70S ribosome by tetracyclines

Devarkar, S.C.Lomakin, I.B.Bunick, C.G.

(2026) Nat Commun 

Macromolecule Content 

  • Total Structure Weight: 2,282.41 kDa 
  • Atom Count: 144,663 
  • Modeled Residue Count: 10,366 
  • Deposited Residue Count: 11,163 
  • Unique protein chains: 49
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 0]56Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2C6LJM0 (Cutibacterium acnes)
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 1]44Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7IDI8 (Cutibacterium acnes)
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35C [auth 2]68Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for Q6A7V2 (Cutibacterium acnes (strain DSM 16379 / KPA171202))
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 3]37Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7JN22 (Cutibacterium acnes)
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31E [auth 4]69Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7JUW7 (Cutibacterium acnes)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth B]283Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I756 (Cutibacterium acnes)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4I [auth D]201Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7JMY9 (Cutibacterium acnes)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5J [auth E]215Cutibacterium acnesMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6K [auth F]96Cutibacterium acnesMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3L [auth G]269Cutibacterium acnesMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8M [auth H]135Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7ITQ7 (Cutibacterium acnes)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7N [auth I]156Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7ITZ4 (Cutibacterium acnes)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9O [auth J]173Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7JN42 (Cutibacterium acnes)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11P [auth K]135Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I645 (Cutibacterium acnes)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12Q [auth L]123Cutibacterium acnesMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10R [auth M]103Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for Q6A6M5 (Cutibacterium acnes (strain DSM 16379 / KPA171202))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13S [auth N]123Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2C6LKT6 (Cutibacterium acnes)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15T [auth O]87Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I743 (Cutibacterium acnes)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16U [auth P]147Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7IXM7 (Cutibacterium acnes)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17V [auth Q]90Cutibacterium acnesMutation(s): 0 
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Find proteins for A0A2B7JMS7 (Cutibacterium acnes)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18W [auth R]79Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2C6LI71 (Cutibacterium acnes)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZX [auth S]61Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7JMX1 (Cutibacterium acnes)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20Y [auth T]88Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I592 (Cutibacterium acnes)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19Z [auth U]93Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7ITR7 (Cutibacterium acnes)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein bL37AA [auth V]24Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A9Y2YAG1 (Cutibacterium acnes)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
AURKAIP1/COX24 domain-containing proteinBA [auth X]33Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A3N4D6F2 (Arachnia propionica)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2FA [auth c]278Cutibacterium acnesMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3GA [auth d]223Cutibacterium acnesMutation(s): 0 
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Find proteins for A0A1G9KW65 (Cutibacterium acnes)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4HA [auth e]301Cutibacterium acnesMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5IA [auth f]210Cutibacterium acnesMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6JA [auth g]180Cutibacterium acnesMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13KA [auth i]147Cutibacterium acnesMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14LA [auth j]122Cutibacterium acnesMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15MA [auth k]146Cutibacterium acnesMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16NA [auth l]139Cutibacterium acnesMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17OA [auth m]187Cutibacterium acnesMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PA [auth n]127Cutibacterium acnesMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19QA [auth o]117Cutibacterium acnesMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20RA [auth p]123Cutibacterium acnesMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21SA [auth q]102Cutibacterium acnesMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22TA [auth r]153Cutibacterium acnesMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23UA [auth s]102Cutibacterium acnesMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24VA [auth t]122Cutibacterium acnesMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25WA [auth u]205Cutibacterium acnesMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27XA [auth v]89Cutibacterium acnesMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L28YA [auth w]61Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I7B7 (Cutibacterium acnes)
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UniProt GroupA0A2B7I7B7
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Reference Sequence
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29ZA [auth x]77Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7JB12 (Cutibacterium acnes)
Explore A0A2B7JB12 
Go to UniProtKB:  A0A2B7JB12
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UniProt GroupA0A2B7JB12
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AB [auth y]60Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I5Y4 (Cutibacterium acnes)
Explore A0A2B7I5Y4 
Go to UniProtKB:  A0A2B7I5Y4
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UniProt GroupA0A2B7I5Y4
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Reference Sequence
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BB [auth z]63Cutibacterium acnesMutation(s): 0 
UniProt
Find proteins for A0A2B7I771 (Cutibacterium acnes)
Explore A0A2B7I771 
Go to UniProtKB:  A0A2B7I771
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2B7I771
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S rRNAF [auth A]1,537Cutibacterium acnes
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Entity ID: 8
MoleculeChains LengthOrganismImage
initiator tRNA Met (76-MER)H [auth C]76Escherichia coli
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Entity ID: 29
MoleculeChains LengthOrganismImage
mRNA 32MFCA [auth Y]22Thermus thermophilus
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Entity ID: 30
MoleculeChains LengthOrganismImage
23S rRNADA [auth a]3,086Cutibacterium acnes
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Entity ID: 31
MoleculeChains LengthOrganismImage
5S rRNAEA [auth b]120Cutibacterium acnes
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DXT
(Subject of Investigation/LOI)

Query on DXT



Download:Ideal Coordinates CCD File
CE [auth a]
JE [auth a]
MM [auth r]
NM [auth s]
RE [auth a]
CE [auth a],
JE [auth a],
MM [auth r],
NM [auth s],
RE [auth a],
TB [auth A],
ZE [auth a]
(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
C22 H24 N2 O8
JBIWCJUYHHGXTC-AKNGSSGZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CB [auth 0]
DB [auth 3]
EB [auth 4]
FD [auth S]
OM [auth w]
CB [auth 0],
DB [auth 3],
EB [auth 4],
FD [auth S],
OM [auth w],
PM [auth z]
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 a],
AM [auth a],
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 a],
BM [auth a],
CC [auth A],
CD [auth A],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth a],
CL [auth a],
CM [auth a],
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 a],
DM [auth a],
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 a],
EM [auth a],
FB [auth A],
FC [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 a],
FM [auth a],
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 a],
GM [auth b],
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 a],
HM [auth b],
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 a],
IM [auth c],
JB [auth A],
JC [auth A],
JD [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
JI [auth a],
JJ [auth a],
JK [auth a],
JL [auth a],
JM [auth d],
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 a],
KM [auth k],
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 a],
LM [auth o],
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 a],
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 a],
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 a],
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 a],
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 a],
RB [auth A],
RC [auth A],
RD [auth a],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
RK [auth a],
RL [auth a],
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 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 a],
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 a],
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],
VK [auth a],
VL [auth a],
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 a],
WL [auth a],
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 a],
XL [auth a],
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 a],
YL [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth a],
ZK [auth a],
ZL [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release