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Crystal structure of NQO1 with dicoumarol

Analyse Crystal structure of NQO1 with dicoumarol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F1O
Type: protein
Length: 2,184 residues
Chains: 8
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: DTC, FAD
Pockets: 18 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	273	37% helix, 16% strand	P15559

Ligands and binding sites

DTC · Bishydroxy[2h-1-benzopyran-2-one,1,2-benzopyrone] · ligand · 8 copies · chains A, C, B, D, E, F, G, H
FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, C, B, D, G, H, E, F

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

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.86	0.87	113	empty
2	624	0.80	0.85	68	FAD, DTC
3	107	0.80	0.98	21	empty
4	508	0.79	0.86	47	FAD, DTC
5	97	0.79	0.99	19	empty

Interfaces

14 interfaces between chains.

G–H · 2779 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 2775 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 2739 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 2688 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 313 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2F1O · Crystal Structure of NQO1 with Dicoumarol · the same entry in another collection · chain H against H, 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 2F1O · PDBe 2F1O · UniProt P15559

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