MolNFT v1 · #142728 · protein

Rat xanthine oxidoreductase, D428E variant

6ADJ · Xanthine DEHYDROGENASE/OXIDASE: “Rat xanthine oxidoreductase, D428E variant”. X-ray diffraction, 3 ligands (FES, FAD, CA), 20 pockets (best druggability 0.89). MolNFT v1 #142728 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6ADJ
Type: protein
Length: 2,583 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xanthine DEHYDROGENASE/OXIDASE
EC: 1.17.1.4, 1.17.3.2
UniProt: P22985
Ligands: FES, FAD, CA
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2)	protein	1297	34% helix, 23% strand	P22985
B	Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2)	protein	1286	33% helix, 23% strand	P22985

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B
FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	995	0.89	0.90	115	FAD
2	1179	0.85	0.86	143	empty
3	913	0.84	0.86	95	FAD
4	145	0.81	0.98	33	empty
5	154	0.81	0.97	35	empty

Interfaces

1 interface between chains.

A–B · 2727 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

6ADJ · Rat Xanthine oxidoreductase, D428E variant · the same entry in another collection · chain A against A, TM-score 1.00
P22985 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P22985) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P22985
Elsewhere: RCSB PDB 6ADJ · PDBe 6ADJ · UniProt P22985

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