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Structure of human NAD(P) H:QUINONE oxidoreductase in complex with N- (2-BROMOPHENYL)PYRROLIDINE-1-sulfonamide

Analyse Structure of human NAD(P) H:QUINONE oxidoreductase in complex with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FY4
Type: protein
Length: 1,080 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(P)H dehydrogenase [quinone] 1
EC: 1.6.5.2
UniProt: P15559
Ligands: FAD, EAW
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	270	39% helix, 16% strand	P15559

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
EAW · N-(2-bromophenyl)pyrrolidine-1-sulfonamide · ligand · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1037	0.86	0.87	108	empty
2	766	0.77	0.81	51	EAW, FAD
3	554	0.77	0.83	51	FAD
4	70	0.75	0.99	18	empty
5	547	0.75	0.82	51	FAD

Interfaces

5 interfaces between chains.

C–D · 2805 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2716 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 493 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 419 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 117 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6FY4 · Structure of human NAD(P) H:qui oxidoreductase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P15559 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase [quinone] 1 (P15559) · 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 P15559
Elsewhere: RCSB PDB 6FY4 · PDBe 6FY4 · UniProt P15559

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