9FQ7 | pdb_00009fq7

Perkinsus marinus Respiratory supercomplex CII2CIII2CIV2 in c1 sate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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

Perkinsus marinus Respiratory supercomplex CII2CIII2CIV2 in c1 sate

Wu, F.Amunts, A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialA [auth 2M],
K [auth 2m]
604Perkinsus marinusMutation(s): 0 
EC: 1.3.5.1
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialB [auth 2N],
L [auth 2n]
259Perkinsus marinusMutation(s): 0 
EC: 1.3.5.1
UniProt
Find proteins for C5LYT4 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SDHGC [auth 2O],
M [auth 2o]
160Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinD [auth 2P],
N [auth 2p]
158Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like proteinE [auth 2Q],
O [auth 2q]
69Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SDHHF [auth 2R],
P [auth 2r]
117Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DUF6827 domain-containing proteinG [auth 2S],
Q [auth 2s]
164Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5L1Y6 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Rab-GAP TBC domain-containing proteinH [auth 2T],
R [auth 2t]
82Perkinsus marinusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
SDHCI [auth 2U],
S [auth 2u]
48Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SDHIJ [auth 2V],
T [auth 2v]
86Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ISPR2U [auth 30]173Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ISPR1V [auth 31]159Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial processing peptidase beta subunitIA [auth 3a],
W [auth 3A]
454Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-MPPJA [auth 3b],
X [auth 3B]
496Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
CytC1KA [auth 3c],
Y [auth 3C]
242Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
QCR8LA [auth 3d],
Z [auth 3D]
95Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
QCR9AA [auth 3E],
MA [auth 3e]
92Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
QCR10BA [auth 3F],
NA [auth 3f]
84Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bCA [auth 3G],
OA [auth 3g]
354Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase, iron-sulfur subunit, putativeDA [auth 3H],
PA [auth 3h]
326Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 14kD subunit, putativeEA [auth 3I],
QA [auth 3i]
176Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putativeFA [auth 3J],
RA [auth 3j]
92Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
QCR11GA [auth 3K],
SA [auth 3k]
79Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinaseHA [auth 3L],
TA [auth 3l]
68Perkinsus marinusMutation(s): 0 
EC: 2.7.11.1
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3UA [auth 40],
VA [auth 41]
230Perkinsus marinusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6BWA [auth 4A],
WB [auth 4a]
100Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase M14 carboxypeptidase A domain-containing proteinXA [auth 4B],
XB [auth 4b]
93Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 40YA [auth 4C],
YB [auth 4c]
75Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 34ZA [auth 4D],
ZB [auth 4d]
90Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Merozoite surface protein, putativeAB [auth 4E],
AC [auth 4e]
152Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin, putativeBB [auth 4F],
BC [auth 4f]
85Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 33CB [auth 4G],
CC [auth 4g]
100Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 30DB [auth 4H],
DC [auth 4h]
141Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CEB [auth 4I],
EC [auth 4i]
196Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 24FB [auth 4J],
FC [auth 4j]
186Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 37GB [auth 4K],
GC [auth 4k]
93Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7AHB [auth 4L],
HC [auth 4l]
122Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 35IB [auth 4M],
IC [auth 4m]
99Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide IIJB [auth 4N],
JC [auth 4n]
131Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
GINS subunit domain-containing proteinKB [auth 4O],
KC [auth 4o]
47Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome oxidase subunit II copper A binding domain-containing proteinLB [auth 4P],
LC [auth 4p]
180Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1MB [auth 4Q],
MC [auth 4q]
459Perkinsus marinusMutation(s): 0 
EC: 7.1.1.9
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 32NB [auth 4R],
NC [auth 4r]
103Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7COB [auth 4S],
OC [auth 4s]
65Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5L3V7 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13PB [auth 4T],
PC [auth 4t]
121Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5K4P8 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Amino acid transporter transmembrane domain-containing proteinQB [auth 4U],
QC [auth 4u]
91Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LG64 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4RB [auth 4V],
RC [auth 4v]
185Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LR54 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 19SB [auth 4W],
SC [auth 4w]
141Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5L0W2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome Coxidase subunit, putativeTB [auth 4X],
TC [auth 4x]
226Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LUB2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 18UB [auth 4Y],
UC [auth 4y]
107Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LUI5 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 31VB [auth 4Z],
VC [auth 4z]
186Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LYX8 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AE [auth 2p]
AF [auth 3I]
AG [auth 3l]
BE [auth 2q]
BF [auth 3I]
AE [auth 2p],
AF [auth 3I],
AG [auth 3l],
BE [auth 2q],
BF [auth 3I],
BG [auth 3l],
BI [auth 4m],
CF [auth 3L],
DF [auth 3L],
DI [auth 4o],
ED [auth 2O],
EF [auth 3L],
GE [auth 2t],
GI [auth 4q],
HD [auth 2P],
HH [auth 4S],
ID [auth 2Q],
IF [auth 3e],
JF [auth 3e],
JG [auth 41],
KE [auth 3D],
KH [auth 4U],
LE [auth 3D],
ME [auth 3E],
MG [auth 4E],
MH [auth 4W],
NG [auth 4E],
OD [auth 2T],
OF [auth 3g],
OI [auth 4s],
PE [auth 3G],
PF [auth 3g],
PG [auth 4F],
PI [auth 4t],
QE [auth 3G],
QF [auth 3g],
QG [auth 4J],
QH [auth 4Z],
RF [auth 3g],
RG [auth 4K],
SG [auth 4L],
TG [auth 4M],
TH [auth 4e],
UD [auth 2o],
UH [auth 4e],
VG [auth 4O],
VH [auth 4f],
WE [auth 3H],
WF [auth 3h],
WI [auth 4z],
XE [auth 3H],
XG [auth 4Q],
XH [auth 4g],
XI [auth 4z],
YF [auth 3i],
YG [auth 4Q],
YH [auth 4j],
ZE [auth 3I],
ZF [auth 3i],
ZH [auth 4j]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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CH [auth 4Q],
DH [auth 4Q],
KI [auth 4q],
LI [auth 4q]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1
Query on PC1

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CE [auth 2r]
DE [auth 2r]
FD [auth 2P]
FF [auth 3a]
HE [auth 3A]
CE [auth 2r],
DE [auth 2r],
FD [auth 2P],
FF [auth 3a],
HE [auth 3A],
JD [auth 2R],
KD [auth 2R],
KF [auth 3f],
LD [auth 2T],
MD [auth 2T],
OG [auth 4F],
SH [auth 4e],
TE [auth 3H],
UE [auth 3H],
UF [auth 3h],
VD [auth 2o],
VF [auth 3h],
YD [auth 2p]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
FAD (Subject of Investigation/LOI)
Query on FAD

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PD [auth 2m],
WC [auth 2M]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEE
Query on PEE

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AI [auth 4l]
CD [auth 2O]
CG [auth 40]
DD [auth 2O]
DG [auth 40]
AI [auth 4l],
CD [auth 2O],
CG [auth 40],
DD [auth 2O],
DG [auth 40],
EE [auth 2r],
EG [auth 40],
EI [auth 4q],
FE [auth 2t],
FG [auth 40],
FH [auth 4R],
FI [auth 4q],
GD [auth 2P],
GF [auth 3c],
GG [auth 41],
GH [auth 4S],
HG [auth 41],
IE [auth 3C],
IG [auth 41],
LF [auth 3f],
LG [auth 4D],
LH [auth 4W],
ND [auth 2T],
NI [auth 4s],
PH [auth 4Z],
RH [auth 4d],
SI [auth 4w],
VE [auth 3H],
VI [auth 4z],
WD [auth 2o],
WG [auth 4Q],
ZD [auth 2p]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
LPP
Query on LPP

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KG [auth 4C],
OH [auth 4Z],
UI [auth 4z],
WH [auth 4g]
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
HEC
Query on HEC

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HF [auth 3c],
JE [auth 3C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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RE [auth 3G],
SE [auth 3G],
SF [auth 3g],
TF [auth 3g]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4

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RD [auth 2n],
ZC [auth 2N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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AD [auth 2N],
SD [auth 2n]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
UQ1
Query on UQ1

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MF [auth 3g]
NE [auth 3G]
NF [auth 3g]
OE [auth 3G]
XC [auth 2N]
MF [auth 3g],
NE [auth 3G],
NF [auth 3g],
OE [auth 3G],
XC [auth 2N],
XD [auth 2p]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FES
Query on FES

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QD [auth 2n],
XF [auth 3h],
YC [auth 2N],
YE [auth 3H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA
Query on CUA

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CI [auth 4n],
UG [auth 4N]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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IH [auth 4T]
JH [auth 4T]
NH [auth 4X]
QI [auth 4t]
RI [auth 4t]
IH [auth 4T],
JH [auth 4T],
NH [auth 4X],
QI [auth 4t],
RI [auth 4t],
TI [auth 4x]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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AH [auth 4Q],
HI [auth 4q]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
K
Query on K

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BD [auth 2N],
JI [auth 4q],
TD [auth 2n],
ZG [auth 4Q]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
PER
Query on PER

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EH [auth 4Q],
MI [auth 4q]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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BH [auth 4Q],
II [auth 4q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2018-StG-805230

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release