9BUH | pdb_00009buh

Cryo-EM structure of respiratory supercomplex I III IV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Cryo-EM structure of respiratory supercomplex I III IV

Zhang, Z.Maharjan, R.Tringides, M.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C74Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7B [auth t]137Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialC [auth F]123Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12D [auth K]145Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialE [auth U]357Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3F [auth Z]114Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialG [auth a]189Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2H [auth i]347Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6I [auth m]175Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9J [auth p]221Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4K [auth q]459Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8L [auth Aa],
XB [auth z]
82Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialBA [auth 0],
M [auth Ab]
91Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 7.2 kDa proteinCA [auth 1],
N [auth Ac]
64Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10EA [auth 3],
O [auth Ad]
56Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8P [auth Ag]70Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialQ [auth Ah]80Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7BR [auth Ai]80Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialS [auth Aj]63Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1T [auth Ak]514Sus scrofaMutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2U [auth Al]228Sus scrofaMutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3V [auth Am]261Sus scrofaMutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4W [auth An]169Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialX [auth Ao]152Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialY [auth Ap]129Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2Z [auth Aq]97Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunitAA [auth Ar]86Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1AC [auth Ae],
BC [auth Af],
DA [auth 2],
FA [auth 4]
299Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialGA [auth 5],
SB [auth u]
480Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialHA [auth 6],
TB [auth v]
453Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bIA [auth 7],
UB [auth w]
379Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1JA [auth 8],
VB [auth x]
326Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7KA [auth 9],
WB [auth y]
111Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialLA [auth B]464Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialMA [auth C]469Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialNA [auth D]264Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialOA [auth E]249Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialPA [auth G]727Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A287ARY3 (Sus scrofa)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialQA [auth H]212Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A286ZUN9 (Sus scrofa)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialRA [auth I]258Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialSA [auth J]175Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialTA [auth L]372Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7UA [auth M]113Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8W4F7N8 (Sus scrofa)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1VA [auth N]116Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinWA [auth O],
YB [auth X]
156Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2XA [auth P]99Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1FN21 (Sus scrofa)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6YA [auth Q]154Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1ZA [auth S]70Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0TJQ4 (Sus scrofa)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3AB [auth T]169Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0Q6N1 (Sus scrofa)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11BB [auth V]141Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LGM4 (Sus scrofa)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A13CB [auth W]144Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0K655 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B2DB [auth Y]105Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1G9F4 (Sus scrofa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6EB [auth b]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480KM09 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialFB [auth c]186Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RWL7 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10GB [auth d]176Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0R7A9 (Sus scrofa)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialHB [auth e]154Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1EYI7 (Sus scrofa)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialIB [auth f]76Sus scrofaMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2JB [auth g]122Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JRW3 (Sus scrofa)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5KB [auth h]106Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VX77 (Sus scrofa)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3LB [auth j]115Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79880 (Sus scrofa)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LMB [auth k]98Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for P56632 (Sus scrofa)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5NB [auth l]606Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q9TDR1 (Sus scrofa)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1OB [auth n]58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4PB [auth o]129Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1QB [auth r]318Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O79874 (Sus scrofa)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8RB [auth s]249Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialZB [auth R]110Sus scrofaMutation(s): 0 
UniProt
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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CC [auth Ak],
DC [auth Ak]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
NDP
Query on NDP

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SC [auth L]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC
Query on HEC

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IC [auth 8],
WC [auth x]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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GC [auth 7],
HC [auth 7],
UC [auth w],
VC [auth w]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZMP
Query on ZMP

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TC [auth Q]S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

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JC [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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KC [auth B]
MC [auth G]
NC [auth G]
PC [auth H]
QC [auth H]
KC [auth B],
MC [auth G],
NC [auth G],
PC [auth H],
QC [auth H],
RC [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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EC [auth 2],
FC [auth 4],
LC [auth E],
OC [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


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: 2025-05-21
    Type: Initial release