MolNFT v1 · #25096 · protein

Crystal structure of alanine racemase from D-cycloserine producing streptomyces lavendulae

1VFH: “Crystal structure of alanine racemase from D-cycloserine producing streptomyces lavendulae”. X-ray diffraction, 1 ligand (PLP), 2 pockets (best druggability 0.54). MolNFT v1 #25096 on GenesisL1: 3D structure, binding sites and…

PDB: 1VFH
Type: protein
Length: 382 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanine racemase
EC: 5.1.1.1
UniProt: Q65YW7
Ligands: PLP
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alanine racemase (EC 5.1.1.1)	protein	382	36% helix, 23% strand	Q65YW7

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.54	0.78	30	PLP
2	83	0.54	0.85	26	empty

Modifications

Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, carboxylation).

Compared structures

1VFH · Crystal structure of alanine racemase from D-cycloserine producing Streptomyces lavendulae · 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 Q65YW7
Elsewhere: RCSB PDB 1VFH · PDBe 1VFH · UniProt Q65YW7

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