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Crystal structure of quinone reductase II

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

PDB: 2QX8
Type: protein
Length: 460 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosyldihydronicotinamide dehydrogenase [quinone]
EC: 1.10.99.2
UniProt: P16083
Ligands: FAD, ML2, ZN, CL
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2)	protein	230	40% helix, 16% strand	P16083

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
ML2 · N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	96	0.51	0.83	30	empty
2	69	0.48	0.84	24	empty
3	72	0.32	0.74	18	empty
4	52	0.27	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 549 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2QX8 · Crystal Structure of Qui Reductase II · the same entry in another collection · chain A against A, TM-score 1.00
P16083 · AlphaFold monomer V2.0 prediction for ribosyldihydronicotinamide dehydrogenase [quinone]… · 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 P16083
Elsewhere: RCSB PDB 2QX8 · PDBe 2QX8 · UniProt P16083

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