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 9FQ7 | pdb_00009fq7

Perkinsus marinus Respiratory supercomplex CII2CIII2CIV2 in c1 state


Experimental Data Snapshot

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

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This is version 2.0 of the entry. See complete history. 

Literature

Perkinsus marinus Respiratory supercomplex CII2CIII2CIV2 in c1 sate

Wu, F., Amunts, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 2,058.83 kDa 
  • Atom Count: 142,971 
  • Modeled Residue Count: 16,544 
  • Deposited Residue Count: 16,550 
  • Unique protein chains: 51

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
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Reference Sequence
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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
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SDHGC [auth 2O],
M [auth 2o]
160Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5KTH2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane proteinD [auth 2P],
N [auth 2p]
158Perkinsus marinusMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-like proteinE [auth 2Q],
O [auth 2q]
69Perkinsus marinusMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
SDHHF [auth 2R],
P [auth 2r]
117Perkinsus marinusMutation(s): 0 
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
SDHCI [auth 2U],
S [auth 2u]
48Perkinsus marinusMutation(s): 0 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
SDHIJ [auth 2V],
T [auth 2v]
86Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LCL6 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
ISPR2U [auth 30]173Perkinsus marinusMutation(s): 0 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
ISPR1V [auth 31]159Perkinsus marinusMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial processing peptidase beta subunitIA [auth 3a],
W [auth 3A]
454Perkinsus marinusMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-MPPJA [auth 3b],
X [auth 3B]
496Perkinsus marinusMutation(s): 0 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
CytC1KA [auth 3c],
Y [auth 3C]
242Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5K8N0 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
QCR8LA [auth 3d],
Z [auth 3D]
95Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5L848 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
QCR9AA [auth 3E],
MA [auth 3e]
92Perkinsus marinusMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
QCR10BA [auth 3F],
NA [auth 3f]
84Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5KTV6 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bCA [auth 3G],
OA [auth 3g]
354Perkinsus marinusMutation(s): 0 
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Reference Sequence
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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 
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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
Find proteins for C5LWC5 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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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 
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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
Find proteins for C5LDF5 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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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 
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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
Find proteins for C5KED7 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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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
Find proteins for C5L7H1 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 34ZA [auth 4D],
ZB [auth 4d]
90Perkinsus marinusMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Merozoite surface protein, putativeAB [auth 4E],
AC [auth 4e]
152Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5L0U1 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin, putativeBB [auth 4F],
BC [auth 4f]
85Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5KBY9 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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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
Find proteins for C5KJE7 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 30DB [auth 4H],
DC [auth 4h]
141Perkinsus marinusMutation(s): 0 
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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 
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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
Find proteins for C5KST9 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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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
Find proteins for C5KPD1 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 35IB [auth 4M],
IC [auth 4m]
99Perkinsus marinusMutation(s): 0 
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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 
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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
Find proteins for C5KSX3 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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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
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13PB [auth 4T],
PC [auth 4t]
121Perkinsus marinusMutation(s): 0 
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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
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4RB [auth 4V],
RC [auth 4v]
185Perkinsus marinusMutation(s): 0 
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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
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome Coxidase subunit, putativeTB [auth 4X],
TC [auth 4x]
226Perkinsus marinusMutation(s): 0 
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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
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 31VB [auth 4Z],
VC [auth 4z]
186Perkinsus marinusMutation(s): 0 
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Reference Sequence

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

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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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
PD [auth 2m],
WC [auth 2M]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEE

Query on PEE



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
HF [auth 3c],
JE [auth 3C]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
HEM

Query on HEM



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
RD [auth 2n],
ZC [auth 2N]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
AD [auth 2N],
SD [auth 2n]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
UQ1

Query on UQ1



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
CI [auth 4n],
UG [auth 4N]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
AH [auth 4Q],
HI [auth 4q]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
BD [auth 2N],
JI [auth 4q],
TD [auth 2n],
ZG [auth 4Q]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
PER

Query on PER



Download:Ideal Coordinates CCD File
EH [auth 4Q],
MI [auth 4q]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BH [auth 4Q],
II [auth 4q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Non-standard Monomers  1 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2

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
  • Version 2.0: 2026-09-02
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary