MolNFT v2 · #202324 · protein

Complex I from Ovis aries at pH9, Open state

7ZDP: “Complex I from Ovis aries at pH9, Open state”. Electron microscopy at 3.88, 10 ligands (SF4, ZMP, FES). MolNFT v2 #202324 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ZDP
Type: protein
Length: 8,160 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.88
Source: Ovis aries
UniProt: A0A7M4DUF9, O78753, O78747, O78757, O78754, O78756, O78755, O78748, W5PAR2, A0A6P3E6Y9, W5NQT7, A0A6P3EAP5, A0A6P3EI17, W5QBF5, A0A836D7R1, W5NYM7, A0A6P3E8V0, W5P9Q8, W5QF73, A0A6P3E975, W5PZE3, W5P5V3, W5PGA3, A0A6P3EC72, W5Q1B0, A0A836CQA7, A0A6P3EDV0, A0A7M4DUG1, A0A7M4DUG2, A0A835ZPN7, W5NRY1, W5QB34, A0A6P3EKX5, A0A6P7E4I4, A0A6P3TFB2, A0A836AFZ8, A0A6P7EX23, W5PE07, W5PI58, W5QAH8, W5PNX7, W5QC06, W5P0I2, A0A6P3CXE3
Ligands: SF4, ZMP, FES, AMP, MYR, FMN, NAI, NDP, K, ZN

Structure

electron microscopy · resolution 3.88 · 45 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
4	—	protein	421	—	A0A7M4DUF9
A	—	protein	110	—	O78753
H	—	protein	314	—	O78747
J	—	protein	169	—	O78757
K	—	protein	98	—	O78754
L	—	protein	606	—	O78756
M	—	protein	459	—	O78755
N	—	protein	347	—	O78748
V	—	protein	140	—	W5PAR2
W	—	protein	139	—	A0A6P3E6Y9
X	—	protein	87	—	W5NQT7
Y	—	protein	171	—	A0A6P3EAP5
Z	—	protein	171	—	A0A6P3EI17
k	—	protein	320	—	W5QBF5
l	—	protein	105	—	A0A836D7R1
m	—	protein	80	—	W5NYM7
n	—	protein	79	—	A0A6P3E8V0
o	—	protein	120	—	W5P9Q8
p	—	protein	128	—	W5QF73
q	—	protein	139	—	A0A6P3E975
r	—	protein	99	—	W5PZE3
s	—	protein	122	—	W5P5V3
t	—	protein	177	—	W5PGA3
u	—	protein	65	—	A0A6P3EC72
v	—	protein	155	—	W5Q1B0
w	—	protein	101	—	A0A836CQA7
x	—	protein	49	—	A0A6P3EDV0
y	—	protein	50	—	A0A7M4DUG1
z	—	protein	70	—	A0A7M4DUG2
1	—	protein	430	—	A0A835ZPN7
2	—	protein	213	—	W5NRY1
3	—	protein	688	—	W5QB34
5	—	protein	208	—	A0A6P3EKX5
6	—	protein	156	—	A0A6P7E4I4
9	—	protein	176	—	A0A6P3TFB2
a	—	protein	44	—	A0A836AFZ8
b	—	protein	95	—	A0A6P7EX23
c	—	protein	126	—	W5PE07
d	—	protein	297	—	W5PI58
e	—	protein	86	—	W5QAH8
f	—	protein	113	—	W5PNX7
g	—	protein	114	—	W5QC06
h	—	protein	96	—	W5P0I2
i	—	protein	145	—	A0A6P3CXE3
j	—	protein	82	—	W5NQT7

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 1, 3, 4, 6, 9
ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · 2 copies · chains X, t, g, j
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 2, 3
AMP · Adenosine monophosphate · ligand · chains k
MYR · Myristic acid · ligand · chains L, s, v
FMN · Flavin mononucleotide · ligand · chains 1
NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains 1
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains 6, d
K · Potassium ion · metal · chains 3
ZN · Zinc ion · metal · chains b

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

Compared structures

O78748 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 2 (O78748) · a predicted model of the same protein · chain N against A, TM-score 0.99
O78755 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 4 (O78755) · a predicted model of the same protein · chain M against A, TM-score 0.99
O78747 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 1 (O78747) · a predicted model of the same protein · chain H against A, TM-score 0.98
O78756 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 5 (O78756) · a predicted model of the same protein · chain L against A, TM-score 0.98
O78757 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 6 (O78757) · a predicted model of the same protein · chain J against A, TM-score 0.89
O78753 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 3 (O78753) · a predicted model of the same protein · chain A against A, TM-score 0.78

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