Research workbench
Crystal structure of the alanine racemase BSU17640 from bacillus subtilis in the presence of hepes
Analyse Crystal structure of the alanine racemase BSU17640 from bacillus subtilis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q70
- Type
- protein
- Length
- 772 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase 2
- EC
- 5.1.1.1
- UniProt
- P94494
- Ligands
- PLP, MG, CL
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase 2 (EC 5.1.1.1) | protein | 386 | 34% helix, 26% strand | P94494 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal
- 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.77 | 0.89 | 49 | CL, MG |
| 2 | 226 | 0.74 | 0.89 | 56 | PLP, CL |
| 3 | 204 | 0.71 | 0.88 | 52 | PLP, CL |
| 4 | 218 | 0.49 | 0.75 | 39 | empty |
| 5 | 135 | 0.47 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 3175 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 6Q70 · Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence… · the same entry in another collection · chain A against A, TM-score 1.00
- P94494 · AlphaFold monomer V2.0 prediction for alanine racemase 2 (P94494) · a predicted model of the same protein · chain B 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 P94494
- Elsewhere: RCSB PDB 6Q70 · PDBe 6Q70 · UniProt P94494
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