Research workbench

Complex I from Ovis aries at pH9, Open state

Analyse Complex I from Ovis aries at pH9, Open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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
Molecule: Complex I-49kD; NADH-ubiquinone oxidoreductase chain 3; NADH-ubiquinone oxidoreductase…
EC: 7.1.1.2
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
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.88 · 45 distinct chains · 51% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
4	Complex I-49kD	protein	421	44% helix, 12% strand	A0A7M4DUF9
A	NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2)	protein	110	67% helix, 0% strand	O78753
H	NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2)	protein	314	67% helix, 0% strand	O78747
J	NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2)	protein	169	66% helix, 4% strand	O78757
K	NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2)	protein	98	76% helix, 0% strand	O78754
L	NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2)	protein	606	74% helix, 4% strand	O78756
M	NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2)	protein	459	70% helix, 2% strand	O78755
N	NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2)	protein	347	70% helix, 1% strand	O78748
V	Complex I-B14.7	protein	140	77% helix, 0% strand	W5PAR2
W	Complex I-SGDH	protein	139	60% helix, 2% strand	A0A6P3E6Y9
X	Acyl carrier protein	protein	87	51% helix, 0% strand	W5NQT7
Y	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	protein	171	49% helix, 2% strand	A0A6P3EAP5
Z	Complex I-PDSW	protein	171	67% helix, 2% strand	A0A6P3EI17
k	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	protein	320	46% helix, 7% strand	W5QBF5
l	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	protein	105	61% helix, 0% strand	A0A836D7R1
m	Complex I-B9	protein	80	53% helix, 3% strand	W5NYM7
n	Complex I-B12	protein	79	47% helix, 0% strand	A0A6P3E8V0
o	NADH dehydrogenase [ubiquinone] 1 subunit C2	protein	120	55% helix, 1% strand	W5P9Q8
p	NADH:ubiquinone oxidoreductase subunit B4	protein	128	59% helix, 2% strand	W5QF73
q	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13	protein	139	56% helix, 1% strand	A0A6P3E975
r	Mitochondrial complex I, B17 subunit	protein	99	35% helix, 5% strand	W5PZE3
s	Complex I-B18	protein	122	59% helix, 1% strand	W5P5V3
t	Complex I-B22	protein	177	56% helix, 0% strand	W5PGA3
u	Complex I-AGGG	protein	65	46% helix, 3% strand	A0A6P3EC72
v	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	protein	155	27% helix, 4% strand	W5Q1B0
w	Complex I-ESSS	protein	101	49% helix, 2% strand	A0A836CQA7
x	Complex I-KFYI	protein	49	67% helix, 0% strand	A0A6P3EDV0
y	Complex I-MNLL	protein	50	40% helix, 0% strand	A0A7M4DUG1
z	Complex I-MWFE	protein	70	63% helix, 0% strand	A0A7M4DUG2
1	NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2)	protein	430	46% helix, 14% strand	A0A835ZPN7
2	NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	protein	213	35% helix, 11% strand	W5NRY1
3	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	protein	688	32% helix, 16% strand	W5QB34
5	Complex I-30kD	protein	208	21% helix, 26% strand	A0A6P3EKX5
6	Complex I-20kD	protein	156	49% helix, 12% strand	A0A6P7E4I4
9	Complex I-23kD	protein	176	38% helix, 17% strand	A0A6P3TFB2
a	Complex I-9kD	protein	44	36% helix, 0% strand	A0A836AFZ8
b	NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	protein	95	15% helix, 20% strand	A0A6P7EX23
c	NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	protein	126	14% helix, 20% strand	W5PE07
d	NADH:ubiquinone oxidoreductase subunit A9	protein	297	36% helix, 14% strand	W5PI58
e	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	protein	86	37% helix, 30% strand	W5QAH8
f	Complex I subunit B13	protein	113	55% helix, 0% strand	W5PNX7
g	Complex I-B14	protein	114	61% helix, 2% strand	W5QC06
h	Mitochondrial complex I, B14.5a subunit	protein	96	18% helix, 5% strand	W5P0I2
i	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	protein	145	22% helix, 12% strand	A0A6P3CXE3
j	Acyl carrier protein	protein	82	49% helix, 0% strand	W5NQT7

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 1, 4, 3, 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 1, 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.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.89	0.90	116	empty
2	1016	0.88	0.89	99	empty
3	576	0.86	0.91	68	empty
4	1150	0.86	0.87	137	ZMP
5	967	0.85	0.87	97	empty

Interfaces

202 interfaces between chains.

1–2 · 3205 Å² buried · 39 hydrogen bonds · protein-protein
A–H · 2957 Å² buried · 9 hydrogen bonds · protein-protein
J–K · 2837 Å² buried · 9 hydrogen bonds · protein-protein
4–5 · 2782 Å² buried · 27 hydrogen bonds · protein-protein
L–M · 2397 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 modified, 5 disulfide, 2 covalent, 1 lipid (disulfide, formylation, covalent ligand, nonstandard, myristoylation, methylation).

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
O78754 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 4L (O78754) · a predicted model of the same protein · chain K against A, TM-score 0.94
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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