MolNFT v1 · #162830 · protein

Structure of human daspo

6RKF · D-aspartate oxidase: “Structure of human daspo”. X-ray diffraction, 2 ligands (FAD, PO4), 20 pockets (best druggability 0.82). MolNFT v1 #162830 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RKF
Type: protein
Length: 2,003 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-aspartate oxidase
EC: 1.4.3.1
UniProt: Q99489
Ligands: FAD, PO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	D-aspartate oxidase (EC 1.4.3.1)	protein	335	31% helix, 26% strand	Q99489
B	D-aspartate oxidase (EC 1.4.3.1)	protein	334	31% helix, 26% strand	Q99489
D, E, F	D-aspartate oxidase (EC 1.4.3.1)	protein	333	34% helix, 27% strand	Q99489

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
PO4 · Phosphate ion · ion · 2 copies · chains A, B, E, F
GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	584	0.82	0.87	72	FAD, GOL
2	696	0.82	0.86	73	FAD, GOL
3	561	0.81	0.87	64	FAD, GOL
4	698	0.81	0.85	73	FAD, GOL
5	801	0.81	0.84	97	FAD, GOL

Interfaces

8 interfaces between chains.

E–F · 1372 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1370 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1345 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 648 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 646 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6RKF · Structure of human DASPO · the same entry in another collection · chain F against F, TM-score 1.00
Q99489 · AlphaFold monomer V2.0 prediction for D-aspartate oxidase (Q99489) · 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 Q99489
Elsewhere: RCSB PDB 6RKF · PDBe 6RKF · UniProt Q99489

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