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Complex of human NAD(P)H quinone oxidoreductase with 5- methoxy-1,2-dimethyl-3-(4-NITROPHENOXYMETHYL)INDOLE-4,7- dione (ES936)

Analyse Complex of human NAD(P)H quinone oxidoreductase with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KBQ
Type: protein
Length: 1,086 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(P)H dehydrogenase [quinone] 1
EC: 1.6.99.2
UniProt: P15559
Ligands: FAD, 936
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.99.2)	protein	272	40% helix, 16% strand	P15559
B, C	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.99.2)	protein	271	41% helix, 16% strand	P15559

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
936 · 5-methoxy-1,2-dimethyl-3-(4-nitrophenoxymethyl)indole-4,7-dione · ligand · 4 copies · chains A, C, B, D

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

Pockets

6 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	108	0.79	0.98	21	empty
2	595	0.78	0.84	50	FAD, 936
3	564	0.77	0.84	49	936, FAD
4	94	0.77	0.98	20	empty
5	586	0.77	0.83	48	FAD, 936

Interfaces

2 interfaces between chains.

A–C · 2755 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 2724 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

1KBQ · Complex of Human NAD(P)H qui Oxidoreductase 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 B 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 1KBQ · PDBe 1KBQ · UniProt P15559

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