MolNFT v1 · #141166 · protein

Crystal structure of alanine racemase from bacillus pseudofirmus (OF4)

5YYC: “Crystal structure of alanine racemase from bacillus pseudofirmus (OF4)”. X-ray diffraction, 1 ligand (PLP), 10 pockets (best druggability 0.77). MolNFT v1 #141166 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YYC
Type: protein
Length: 736 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanine racemase
EC: 5.1.1.1
UniProt: D3FSP1
Ligands: PLP
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Alanine racemase (EC 5.1.1.1)	protein	368	33% helix, 23% strand	D3FSP1

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, C

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	542	0.77	0.84	74	empty
2	192	0.73	0.89	47	PLP
3	75	0.72	0.96	25	PLP
4	106	0.64	0.89	28	empty
5	71	0.57	0.88	25	empty

Interfaces

1 interface between chains.

A–C · 2915 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

5YYC · Crystal structure of alanine racemase from Bacillus pseudofirmus (OF4) · 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 D3FSP1
Elsewhere: RCSB PDB 5YYC · PDBe 5YYC · UniProt D3FSP1

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