Research workbench

Entire ovine respiratory complex I

Analyse Entire ovine respiratory complex I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LNK
Type: protein
Length: 8,037 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial complex I, 51 kda subunit; Mitochondrial complex I, 24 kda subunit…
UniProt: W5PUX0, W5NRY1, W5QB34, W5PJ73, W5PB27, O78747, O78748, O78753, O78755, O78754, O78756, O78757, W5PI58, W5QAH8, W5PNX7, W5QC06, W5P0I2, B9VGZ9, W5NQT7, W5QBF5, W5NYM7, W5Q5T4, W5PZE3, W5P5V3, W5PGA3, W5PVD7, W5Q1B0, W5PWF1, W5PYA5, W5QHN8
Ligands: SF4, 3PE, PC1, CDL, FES, FMN, NDP, ZMP, PNS, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 45 distinct chains · 48% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Mitochondrial complex I, 51 kda subunit	protein	432	47% helix, 12% strand	W5PUX0
2	Mitochondrial complex I, 24 kda subunit	protein	214	35% helix, 7% strand	W5NRY1
3	Mitochondrial complex I, 75 kda subunit	protein	688	30% helix, 16% strand	W5QB34
4	Mitochondrial complex I, 49 kda subunit	protein	387	50% helix, 11% strand	W5PJ73
5	Mitochondrial complex I, 30 kda subunit	protein	208	19% helix, 26% strand	W5PB27
6	Mitochondrial complex I, psst subunit	protein	155	41% helix, 9% strand	—
9	Mitochondrial complex I, tyky subunit	protein	176	32% helix, 11% strand	—
H	Mitochondrial complex I, ND1 subunit	protein	318	66% helix, 0% strand	O78747
N	Mitochondrial complex I, ND2 subunit	protein	347	69% helix, 1% strand	O78748
A	Mitochondrial complex I, ND3 subunit	protein	115	63% helix, 0% strand	O78753
M	Mitochondrial complex I, ND4 subunit	protein	459	68% helix, 0% strand	O78755
K	Mitochondrial complex I, ND4L subunit	protein	86	76% helix, 0% strand	O78754
L	Mitochondrial complex I, ND5 subunit	protein	599	68% helix, 1% strand	O78756
J	Mitochondrial complex I, ND6 subunit	protein	175	63% helix, 0% strand	O78757
a	Mitochondrial complex I, 10 kda subunit	protein	41	32% helix, 0% strand	—
b	Mitochondrial complex I, 13 kda subunit	protein	95	11% helix, 18% strand	—
c	Mitochondrial complex I, 18 kda subunit	protein	123	15% helix, 11% strand	—
d	Mitochondrial complex I, 39 kda subunit	protein	314	33% helix, 9% strand	W5PI58
e	Mitochondrial complex I, B8 subunit	protein	84	39% helix, 24% strand	W5QAH8
f	Mitochondrial complex I, B13 subunit	protein	112	55% helix, 0% strand	W5PNX7
g	Mitochondrial complex I, B14 subunit	protein	114	62% helix, 0% strand	W5QC06
h	Mitochondrial complex I, B14.5A subunit	protein	95	12% helix, 2% strand	W5P0I2
i	Mitochondrial complex I, B17.2 subunit	protein	144	24% helix, 6% strand	B9VGZ9
j	Acyl carrier protein	protein	85	56% helix, 0% strand	W5NQT7
k	Mitochondrial complex I, 42 kda subunit	protein	320	48% helix, 5% strand	W5QBF5
l	Mitochondrial complex I, 15 kda subunit	protein	95	48% helix, 0% strand	—
m	Mitochondrial complex I, B9 subunit	protein	80	54% helix, 3% strand	W5NYM7
n	Mitochondrial complex I, B12 subunit	protein	74	42% helix, 0% strand	W5Q5T4
o	Mitochondrial complex I, B14.5B subunit	protein	120	53% helix, 1% strand	—
p	Mitochondrial complex I, B15 subunit	protein	112	52% helix, 0% strand	—
q	Mitochondrial complex I, B16.6 subunit	protein	140	51% helix, 0% strand	—
r	Mitochondrial complex I, B17 subunit	protein	93	53% helix, 3% strand	W5PZE3
s	Mitochondrial complex I, B18 subunit	protein	118	53% helix, 2% strand	W5P5V3
t	Mitochondrial complex I, B22 subunit	protein	166	47% helix, 0% strand	W5PGA3
u	Mitochondrial complex I, aggg subunit	protein	66	44% helix, 2% strand	W5PVD7
v	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	protein	143	24% helix, 0% strand	W5Q1B0
w	Mitochondrial complex I, esss subunit	protein	86	47% helix, 0% strand	W5PWF1
x	Mitochondrial complex I, kfyi subunit	protein	48	67% helix, 0% strand	—
y	Mitochondrial complex I, mnll subunit	protein	53	45% helix, 0% strand	—
z	Mitochondrial complex I, mwfe subunit	protein	69	62% helix, 0% strand	—
Z	Mitochondrial complex I, pdsw subunit	protein	171	60% helix, 1% strand	—
Y	Mitochondrial complex I, pgiv subunit	protein	171	44% helix, 1% strand	W5PYA5
X	Acyl carrier protein	protein	88	51% helix, 0% strand	W5NQT7
W	Mitochondrial complex I, sgdh subunit	protein	139	53% helix, 1% strand	W5QHN8
V	Mitochondrial complex I, B14.7 subunit	protein	119	60% helix, 0% strand	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 1, 3, 4, 6, 9
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains 4, 9, H, m, q, A, J, z, N, M, o, x
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains N, k, H, A, J, m, M, o, y, Y, l
CDL · Cardiolipin · ligand · 4 copies · chains M, L, w, W, N, A, J, l, 9, H, h, i, z
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 1, 2, 3
FMN · Flavin mononucleotide · ligand · chains 1
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains 6, d
ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · chains g, j
PNS · 4'-phosphopantetheine · ligand · chains t, X
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	1172	0.89	0.91	119	3PE
2	1003	0.89	0.90	111	empty
3	533	0.88	0.94	80	empty
4	806	0.86	0.89	93	ZMP
5	1167	0.85	0.86	146	empty

Interfaces

191 interfaces between chains.

1–2 · 3209 Å² buried · 34 hydrogen bonds · protein-protein
H–A · 2801 Å² buried · 6 hydrogen bonds · protein-protein
4–5 · 2734 Å² buried · 25 hydrogen bonds · protein-protein
K–J · 2498 Å² buried · 9 hydrogen bonds · protein-protein
3–c · 2307 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 1 cofactor, 1 covalent (disulfide, phosphopantetheinylation, covalent ligand).

Compared structures

5LNK · Entire ovine respiratory complex I · the same entry in another collection · chain j against j, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt W5PUX0
Every structure of UniProt W5NRY1
Every structure of UniProt W5QB34
Every structure of UniProt W5PJ73
Every structure of UniProt W5PB27
Every structure of UniProt O78747
Every structure of UniProt O78748
Every structure of UniProt O78753
Every structure of UniProt O78755
Every structure of UniProt O78754
Every structure of UniProt O78756
Every structure of UniProt O78757
Every structure of UniProt W5PI58
Every structure of UniProt W5QAH8
Every structure of UniProt W5PNX7
Every structure of UniProt W5QC06
Every structure of UniProt W5P0I2
Every structure of UniProt B9VGZ9
Every structure of UniProt W5NQT7
Every structure of UniProt W5QBF5
Every structure of UniProt W5NYM7
Every structure of UniProt W5Q5T4
Every structure of UniProt W5PZE3
Every structure of UniProt W5P5V3
Every structure of UniProt W5PGA3
Every structure of UniProt W5PVD7
Every structure of UniProt W5Q1B0
Every structure of UniProt W5PWF1
Every structure of UniProt W5PYA5
Every structure of UniProt W5QHN8
Elsewhere: RCSB PDB 5LNK · PDBe 5LNK · UniProt W5PUX0 · UniProt W5NRY1 · UniProt W5QB34 · UniProt W5PJ73 · UniProt W5PB27 · UniProt O78747 · UniProt O78748 · UniProt O78753 · UniProt O78755 · UniProt O78754 · UniProt O78756 · UniProt O78757 · UniProt W5PI58 · UniProt W5QAH8 · UniProt W5PNX7 · UniProt W5QC06 · UniProt W5P0I2 · UniProt B9VGZ9 · UniProt W5NQT7 · UniProt W5QBF5 · UniProt W5NYM7 · UniProt W5Q5T4 · UniProt W5PZE3 · UniProt W5P5V3 · UniProt W5PGA3 · UniProt W5PVD7 · UniProt W5Q1B0 · UniProt W5PWF1 · UniProt W5PYA5 · UniProt W5QHN8

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