MolNFT v1 · #161205 · protein
Crystal structure of the alanine racemase BSU17640 from bacillus subtilis in the presence of hepes
6Q70 · Alanine racemase 2: “Crystal structure of the alanine racemase BSU17640 from bacillus subtilis in the presence of hepes”. X-ray diffraction, 3 ligands (PLP, MG, CL), 9 pockets (best druggability 0.77). MolNFT v1 #161205 on…
- 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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