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Crystal structure of alanine racemase from corynebacterium glutamicum

Analyse Crystal structure of alanine racemase from corynebacterium glutamicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DY3
Type: protein
Length: 1,365 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanine racemase
EC: 5.1.1.1
UniProt: Q8RSU9
Ligands: PLP
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alanine racemase (EC 5.1.1.1)	protein	338	33% helix, 24% strand	Q8RSU9
B	Alanine racemase (EC 5.1.1.1)	protein	340	33% helix, 25% strand	Q8RSU9
C	Alanine racemase (EC 5.1.1.1)	protein	343	32% helix, 23% strand	Q8RSU9
D	Alanine racemase (EC 5.1.1.1)	protein	344	33% helix, 23% strand	Q8RSU9

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1079	0.79	0.80	106	PLP
2	444	0.77	0.85	60	PLP
3	349	0.76	0.87	51	PLP
4	132	0.76	0.95	33	empty
5	493	0.75	0.84	57	PLP

Interfaces

6 interfaces between chains.

C–D · 2496 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2361 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 305 Å² buried · 1 hydrogen bond · protein-protein
B–C · 153 Å² buried · 1 hydrogen bond · protein-protein
B–D · 120 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).

Compared structures

2DY3 · Crystal Structure of alanine racemase from Corynebacterium glutamicum · the same entry in another collection · chain D against D, TM-score 1.00
Q8RSU9 · AlphaFold monomer V2.0 prediction for alanine racemase (Q8RSU9) · a predicted model of the same protein · chain C 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 Q8RSU9
Elsewhere: RCSB PDB 2DY3 · PDBe 2DY3 · UniProt Q8RSU9

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