9FZL | pdb_00009fzl

Perkinsus marinus respiratory supercomplex CII2CIII2CIV2 in an intermediate state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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 an intermediate state

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],
XA [auth 2m]
604Perkinsus marinusMutation(s): 0 
EC: 1.3.5.1
UniProt
Find proteins for C5LYE7 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialB [auth 2N],
YA [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],
ZA [auth 2o]
160Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5KTH2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinAB [auth 2p],
D [auth 2P]
158Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LSM2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like proteinBB [auth 2q],
E [auth 2Q]
69Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SDHHCB [auth 2r],
F [auth 2R]
117Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for A0A7J6R9U3 (Perkinsus olseni)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DUF6827 domain-containing proteinDB [auth 2s],
G [auth 2S]
165Perkinsus 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 proteinEB [auth 2t],
H [auth 2T]
82Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Syntaxin-1AFB [auth 2u],
I [auth 2U]
48Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SDHIGB [auth 2v],
J [auth 2V]
87Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial processing peptidase beta subunitHB [auth 3a],
K [auth 3A]
454Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-MPPIB [auth 3b],
L [auth 3B]
496Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Iso-1-cytochrome cJB [auth 3c],
M [auth 3C]
241Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5K8N0 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
QCR8KB [auth 3d],
N [auth 3D]
95Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
QCR9LB [auth 3e],
O [auth 3E]
92Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for A0A7J6MEE8 (Perkinsus chesapeaki)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
QCR10MB [auth 3f],
P [auth 3F]
84Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5KTV6 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bNB [auth 3g],
Q [auth 3G]
354Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase, iron-sulfur subunit, putativeOB [auth 3h],
R [auth 3H]
326Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 14kD subunit, putativePB [auth 3i],
S [auth 3I]
176Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 7.8 kDa protein, putativeQB [auth 3j],
T [auth 3J]
92Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cu-binding proteinRB [auth 3k],
U [auth 3K]
79Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinaseSB [auth 3l],
V [auth 3L]
69Perkinsus 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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3TB [auth 41],
W [auth 40]
230Perkinsus marinusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6BUB [auth 4a],
X [auth 4A]
100Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase M14 carboxypeptidase A domain-containing proteinVB [auth 4b],
Y [auth 4B]
93Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 40WB [auth 4c],
Z [auth 4C]
75Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 34AA [auth 4D],
XB [auth 4d]
90Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Merozoite surface protein, putativeBA [auth 4E],
YB [auth 4e]
152Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin, putativeCA [auth 4F],
ZB [auth 4f]
73Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 33AC [auth 4g],
DA [auth 4G]
100Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 30BC [auth 4h],
EA [auth 4H]
141Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CCC [auth 4i],
FA [auth 4I]
196Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 24DC [auth 4j],
GA [auth 4J]
186Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 37EC [auth 4k],
HA [auth 4K]
93Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7AFC [auth 4l],
IA [auth 4L]
122Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 35GC [auth 4m],
JA [auth 4M]
98Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide IIHC [auth 4n],
KA [auth 4N]
131Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
GINS subunit domain-containing proteinIC [auth 4o],
LA [auth 4O]
47Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2AJC [auth 4p],
MA [auth 4P]
180Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1KC [auth 4q],
NA [auth 4Q]
459Perkinsus marinusMutation(s): 0 
EC: 7.1.1.9
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 32LC [auth 4r],
OA [auth 4R]
103Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7CMC [auth 4s],
PA [auth 4S]
65Perkinsus marinusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13NC [auth 4t],
QA [auth 4T]
121Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5K4P8 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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UniProt GroupC5K4P8
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Amino acid transporter transmembrane domain-containing proteinOC [auth 4u],
RA [auth 4U]
91Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LG64 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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UniProt GroupC5LG64
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4PC [auth 4v],
SA [auth 4V]
185Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LR54 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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UniProt GroupC5LR54
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 19QC [auth 4w],
TA [auth 4W]
141Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5L0W2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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UniProt GroupC5L0W2
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome Coxidase subunit, putativeRC [auth 4x],
UA [auth 4X]
226Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LUB2 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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UniProt GroupC5LUB2
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 18SC [auth 4y],
VA [auth 4Y]
107Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LUI5 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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UniProt GroupC5LUI5
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 31TC [auth 4z],
WA [auth 4Z]
186Perkinsus marinusMutation(s): 0 
UniProt
Find proteins for C5LYX8 (Perkinsus marinus (strain ATCC 50983 / TXsc))
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AE [auth 3G]
AI [auth 4l]
BI [auth 4m]
CD [auth 2O]
CG [auth 2o]
AE [auth 3G],
AI [auth 4l],
BI [auth 4m],
CD [auth 2O],
CG [auth 2o],
DD [auth 2P],
DH [auth 3g],
EE [auth 3H],
GE [auth 3I],
GF [auth 4Q],
GG [auth 2p],
HD [auth 2Q],
HE [auth 3I],
HF [auth 4Q],
HH [auth 3h],
IE [auth 3I],
JE [auth 3L],
JH [auth 3i],
JI [auth 4q],
KE [auth 3L],
KG [auth 2q],
KH [auth 3i],
KI [auth 4q],
LF [auth 4S],
LH [auth 3i],
MD [auth 2U],
MH [auth 3l],
NH [auth 3l],
OI [auth 4s],
PF [auth 4T],
PG [auth 2u],
QF [auth 4U],
RD [auth 3D],
RF [auth 4W],
SD [auth 3D],
SE [auth 4E],
SF [auth 4W],
SI [auth 4t],
TI [auth 4u],
UD [auth 3E],
UE [auth 4J],
UG [auth 3d],
UI [auth 4w],
VD [auth 3E],
VE [auth 4K],
VF [auth 4Z],
VG [auth 3d],
VH [auth 4e],
VI [auth 4w],
WD [auth 3E],
WE [auth 4K],
XE [auth 4L],
XG [auth 3e],
XH [auth 4j],
YE [auth 4M],
YG [auth 3e],
YH [auth 4k],
YI [auth 4z],
ZG [auth 3e],
ZH [auth 4k]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
AJP
Query on AJP

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OE [auth 40],
RH [auth 41]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
HEA
Query on HEA

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DF [auth 4Q],
EF [auth 4Q],
GI [auth 4q],
HI [auth 4q]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1 (Subject of Investigation/LOI)
Query on PC1

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AD [auth 2O]
BD [auth 2O]
EG [auth 2o]
FE [auth 3H]
FG [auth 2o]
AD [auth 2O],
BD [auth 2O],
EG [auth 2o],
FE [auth 3H],
FG [auth 2o],
GD [auth 2P],
IH [auth 3h],
JD [auth 2R],
JG [auth 2p],
LD [auth 2T],
MG [auth 2r],
ND [auth 3A],
OD [auth 3A],
OG [auth 2t],
QG [auth 3a],
RG [auth 3a],
TE [auth 4E],
WH [auth 4e]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
FAD
Query on FAD

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UC [auth 2M],
XF [auth 2m]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEE (Subject of Investigation/LOI)
Query on PEE

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AH [auth 3f]
DG [auth 2o]
ED [auth 2P]
FD [auth 2P]
HG [auth 2p]
AH [auth 3f],
DG [auth 2o],
ED [auth 2P],
FD [auth 2P],
HG [auth 2p],
ID [auth 2R],
IF [auth 4Q],
IG [auth 2p],
JF [auth 4Q],
KF [auth 4R],
LE [auth 40],
LG [auth 2r],
LI [auth 4q],
ME [auth 40],
MF [auth 4S],
MI [auth 4q],
NE [auth 40],
NI [auth 4r],
OH [auth 41],
PH [auth 41],
PI [auth 4s],
QD [auth 3C],
QE [auth 4D],
QH [auth 41],
TF [auth 4W],
TG [auth 3c],
TH [auth 4d],
WF [auth 4Z],
WI [auth 4w],
XD [auth 3F],
ZC [auth 2O],
ZI [auth 4z]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
UQ8
Query on UQ8

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BE [auth 3G]
CE [auth 3G]
EH [auth 3g]
FH [auth 3g]
KD [auth 2S]
BE [auth 3G],
CE [auth 3G],
EH [auth 3g],
FH [auth 3g],
KD [auth 2S],
NG [auth 2s],
TD [auth 3D],
WG [auth 3d]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
LPP (Subject of Investigation/LOI)
Query on LPP

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PE [auth 4C],
RE [auth 4D],
SH [auth 4c],
UH [auth 4d]
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
HEC
Query on HEC

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

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BH [auth 3g],
CH [auth 3g],
YD [auth 3G],
ZD [auth 3G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4

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

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AG [auth 2n],
XC [auth 2N]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES
Query on FES

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DE [auth 3H],
GH [auth 3h],
VC [auth 2N],
YF [auth 2n]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA
Query on CUA

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

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NF [auth 4T]
OF [auth 4T]
QI [auth 4t]
RI [auth 4t]
UF [auth 4X]
NF [auth 4T],
OF [auth 4T],
QI [auth 4t],
RI [auth 4t],
UF [auth 4X],
XI [auth 4x]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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

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BG [auth 2n],
CF [auth 4Q],
FI [auth 4q],
YC [auth 2N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
PER
Query on PER

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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: 2025-07-23
    Type: Initial release