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MolNFT v1 · #189118 · protein

Active state complex I from rotenone dataset

7V31: “Active state complex I from rotenone dataset”. Electron microscopy, 13 ligands (PEE, CDL, PLX). MolNFT v1 #189118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7V31
Type
protein
Length
8,269 residues
Chains
45
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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, CDL, PLX, SF4, 8Q1, UQ, FES, FMN, 970, NDP, ADP, MG, ZN

Structure

electron microscopy · 44 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein433—F1RVN1
B—protein176—A0A287BDC0
C—protein156—I3LK43
E—protein115—A0A480VKQ8
F—protein86—F1RGE3
G, X—protein88—D0G781
H—protein112—A0A5G2RN85
I—protein97—A0A4X1VLA2
J—protein342—A0A480QJC4
K—protein43—A0A4X1TFI3
L—protein125—G8IFA6
M—protein690—F1SHD7
N—protein144—F1SQP4
O—protein217—A0A287BG40
P—protein208—A0A286ZNN4
Q—protein430—A0A480JYS1
S—protein70—K7GR43
T—protein96—F1S031
U—protein83—A0A4X1VQ42
V—protein140—I3LGM4
W—protein142—F1S6Q1
Y—protein67—A0A4X1V766
Z—protein80—A0A287AS93
a—protein138—F1SGC6
b—protein98—Q2EN80
c—protein156—F1RWL7
d—protein175—A0A4X1VYV0
e—protein104——
f—protein49—A1XQS6
g—protein121—A0A480JRW3
h—protein105—F1SV23
i—protein347—O79875
j—protein115—O79880
k—protein98—P56632
l—protein606—Q71K68
m—protein175—O79882
n—protein56—F1SD73
o—protein128—A0A4X1T6M0
p—protein178—A0A4X1T0A8
r—protein459—Q7IIB7
s—protein318—O79874
u—protein171—F1SLR1
v—protein124—F1SCH1
w—protein320—F1SIS9

Ligands and binding sites

  • PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 12 copies · chains B, Q, U, W, s, i, l, r, j, S, m, b, V, c, C, J, v
  • CDL · Cardiolipin · ligand · 10 copies · chains I, N, S, s, V, i, l, o, r, a, b, d, e, c, k, m, g, w, J, n, u
  • 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 · 7 copies · chains C, N, s, J, j, a, e, n, r, g, h, i, m, V, l
  • SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, Q, M
  • 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, p
  • UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · 2 copies · chains J, C, Q, s
  • FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, O
  • FMN · Flavin mononucleotide · ligand · chains A
  • 970 · (2r,6as,12as)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12, 12A-tetrahydrofuro[2',3':7,8][1]benzopyrano[2,3-c][1]benzopyran-6(6ah)-one · ligand · chains C, Q
  • NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains C, J
  • 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

  • 7V31 · Active state complex I from rote dataset · the same entry in another collection · chain L against L, TM-score 1.00

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