GL1X · GenesisL1 explorer

MolNFT v2 · #198588 · protein

Deactive state CI from Q1-NADH dataset, Subclass 1

7W4J: “Deactive state CI from Q1-NADH dataset, Subclass 1”. Electron microscopy at 3.2, 13 ligands (PEE, SF4, PLX). MolNFT v2 #198588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7W4J
Type
protein
Length
8,140 residues
Chains
45
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.2
Source
Sus scrofa
UniProt
F1RVN1, A0A287BDC0, I3LK43, A0A480VKQ8, F1RGE3, D0G781, A0A5G2RN85, A0A4X1VLA2, A0A480QJC4, A0A4X1TFI3, G8IFA6, F1SHD7, F1SQP4, A0A287BG40, A0A286ZNN4, A0A480JYS1, K7GR43, F1S031, A0A4X1VQ42, I3LGM4, F1S6Q1, A0A4X1V766, A0A287AS93, F1SGC6, Q2EN80, F1RWL7, A0A4X1VYV0, A1XQS6, A0A480JRW3, F1SV23, O79875, O79880, P56632, Q71K68, O79882, F1SD73, A0A4X1T6M0, A0A4X1T0A8, Q7IIB7, O79874, F1SLR1, F1SCH1, F1SIS9
Ligands
PEE, SF4, PLX, CDL, 8Q1, FES, FMN, NAI, NDP, UQ, ADP, MG, ZN

Structure

electron microscopy · resolution 3.2 · 44 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein431—F1RVN1
B—protein176—A0A287BDC0
C—protein156—I3LK43
E—protein115—A0A480VKQ8
F—protein86—F1RGE3
G, X—protein88—D0G781
H—protein112—A0A5G2RN85
I—protein97—A0A4X1VLA2
J—protein297—A0A480QJC4
K—protein42—A0A4X1TFI3
L—protein125—G8IFA6
M—protein690—F1SHD7
N—protein144—F1SQP4
O—protein217—A0A287BG40
P—protein208—A0A286ZNN4
Q—protein419—A0A480JYS1
S—protein70—K7GR43
T—protein96—F1S031
U—protein83—A0A4X1VQ42
V—protein140—I3LGM4
W—protein142—F1S6Q1
Y—protein70—A0A4X1V766
Z—protein84—A0A287AS93
a—protein140—F1SGC6
b—protein103—Q2EN80
c—protein156—F1RWL7
d—protein175—A0A4X1VYV0
e—protein107——
f—protein42—A1XQS6
g—protein121—A0A480JRW3
h—protein105—F1SV23
i—protein347—O79875
j—protein99—O79880
k—protein98—P56632
l—protein603—Q71K68
m—protein129—O79882
n—protein56—F1SD73
o—protein128—A0A4X1T6M0
p—protein178—A0A4X1T0A8
r—protein459—Q7IIB7
s—protein303—O79874
u—protein171—F1SLR1
v—protein124—F1SCH1
w—protein320—F1SIS9

Ligands and binding sites

  • PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains U, j, s, Q, i, l, r, C, c, b, S, W, m, V, B
  • SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, Q, M
  • PLX · (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol · ligand · 6 copies · chains C, N, a, e, n, r, g, h, i, j, m, l, V
  • CDL · Cardiolipin · ligand · 6 copies · chains I, N, S, s, V, l, o, r, a, b, d, e, i, w, c, g
  • 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains E, G, X, l, p
  • FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, O
  • FMN · Flavin mononucleotide · ligand · chains A
  • NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
  • NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains C, J
  • UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains C, s
  • ADP · Adenosine-5'-diphosphate · ligand · chains w
  • MG · Magnesium ion · metal · chains M
  • ZN · Zinc ion · metal · chains T

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • O79875 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 2 (O79875) · a predicted model of the same protein · chain i against A, TM-score 0.99
  • O79874 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 1 (O79874) · a predicted model of the same protein · chain s against A, TM-score 0.99
  • P56632 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 4L (P56632) · a predicted model of the same protein · chain k against A, TM-score 0.96
  • O79882 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 6 (O79882) · a predicted model of the same protein · chain m against A, TM-score 0.96
  • O79880 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 3 (O79880) · a predicted model of the same protein · chain j against A, TM-score 0.87

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