MolNFT v1 · #12493 · protein

D-amino acid oxidase from pig kidney

1KIF: “D-amino acid oxidase from pig kidney”. X-ray diffraction, 2 ligands (FAD, BEZ), 20 pockets (best druggability 0.86). MolNFT v1 #12493 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KIF
Type: protein
Length: 2,712 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-amino acid oxidase
EC: 1.4.3.3
UniProt: P00371
Ligands: FAD, BEZ
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	D-amino acid oxidase (EC 1.4.3.3)	protein	339	31% helix, 29% strand	P00371

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
BEZ · Benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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	717	0.86	0.90	113	empty
2	390	0.86	0.94	56	FAD, BEZ
3	380	0.85	0.93	55	FAD, BEZ
4	377	0.85	0.93	57	FAD, BEZ
5	567	0.85	0.90	91	empty

Interfaces

12 interfaces between chains.

B–F · 1602 Å² buried · 16 hydrogen bonds · protein-protein
C–G · 1600 Å² buried · 17 hydrogen bonds · protein-protein
D–H · 1598 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 1586 Å² buried · 16 hydrogen bonds · protein-protein
D–G · 794 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1KIF · D-amino acid oxidase from pig kidney · the same entry in another collection · chain H against H, TM-score 1.00
P00371 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P00371) · 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 P00371
Elsewhere: RCSB PDB 1KIF · PDBe 1KIF · UniProt P00371

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