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Crystal structure of ndh with NADH and quinone

Analyse Crystal structure of ndh with NADH and quinone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G73
Type: protein
Length: 944 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
EC: 1.6.5.9
UniProt: P32340
Ligands: UQ5, FAD, NAI, MG
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9)	protein	472	36% helix, 26% strand	P32340

Ligands and binding sites

UQ5 · 2,3-dimethoxy-5-methyl-6-(3,11,15,19-tetramethyl-eicosa-2,6,10,14,18-pentaenyl)-[1,4]benzoquinone · ligand · 5 copies · chains A, B
FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 11 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	254	0.80	0.92	35	empty
2	866	0.79	0.82	82	UQ5, FAD, MG, NAI
3	1085	0.79	0.80	98	NAI, UQ5, FAD, MG
4	296	0.77	0.89	36	empty
5	84	0.74	0.97	27	empty

Interfaces

1 interface between chains.

A–B · 2194 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4G73 · Crystal structure of NDH with NADH and Qui · the same entry in another collection · chain A against A, TM-score 1.00
P32340 · AlphaFold monomer V2.0 prediction for rotenone-insensitive NADH- ubiquinone… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P32340
Elsewhere: RCSB PDB 4G73 · PDBe 4G73 · UniProt P32340

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