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The crystal structure of alanine racemase from bacillus anthracis (BA0252) with bound L-ala-P
Analyse The crystal structure of alanine racemase from bacillus anthracis (BA0252) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VD9
- Type
- protein
- Length
- 772 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
- IN5, EPC, MG, CL
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase (EC 5.1.1.1) | protein | 386 | 32% helix, 27% strand | Q81VF6 |
Ligands and binding sites
- IN5 · {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid · ligand · 2 copies · chains A, B
- EPC · (1S)-1-[((1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylene)amino]ethylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.77 | 0.90 | 53 | CL, IN5, EPC |
| 2 | 329 | 0.77 | 0.88 | 64 | CL, IN5, EPC |
| 3 | 54 | 0.70 | 0.98 | 26 | empty |
| 4 | 96 | 0.53 | 0.84 | 19 | empty |
| 5 | 95 | 0.52 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3740 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (methylation).
Compared structures
- 2VD9 · The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound… · 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 2VD9 · PDBe 2VD9 · UniProt Q81VF6
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