Research workbench
The crystal structure of alanine racemase from bacillus anthracis (BA0252)
Analyse The crystal structure of alanine racemase from bacillus anthracis (BA0252) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VD8
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q81VF6
- Ligands
- PLP, MG, CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 387 | 31% helix, 26% strand | Q81VF6 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 386 | 32% helix, 26% strand | Q81VF6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.75 | 0.88 | 59 | PLP, CL |
| 2 | 224 | 0.75 | 0.90 | 54 | PLP, CL |
| 3 | 58 | 0.72 | 0.99 | 26 | empty |
| 4 | 95 | 0.56 | 0.85 | 20 | empty |
| 5 | 95 | 0.52 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3748 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 2 cofactor (methylation, pyridoxal phosphate Schiff base).
Compared structures
- 2VD8 · The crystal structure of alanine racemase from Bacillus anthracis (BA0252) · 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 Q81VF6
- Elsewhere: RCSB PDB 2VD8 · PDBe 2VD8 · UniProt Q81VF6
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