MolNFT v1 · #140473 · protein

Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase

5YBW: “Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase”. X-ray diffraction, 4 pockets (best druggability 0.71). MolNFT v1 #140473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YBW
Type: protein
Length: 654 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartate racemase
EC: 5.1.1.13
UniProt: Q2L695
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aspartate racemase (EC 5.1.1.13)	protein	329	46% helix, 16% strand	Q2L695
B	Aspartate racemase (EC 5.1.1.13)	protein	325	43% helix, 15% strand	Q2L695

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	512	0.71	0.80	60	empty
2	501	0.70	0.80	51	empty
3	335	0.66	0.81	40	empty
4	211	0.53	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 954 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cofactor).

Compared structures

5YBW · Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase · the same entry in another collection · 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 Q2L695
Elsewhere: RCSB PDB 5YBW · PDBe 5YBW · UniProt Q2L695

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