MolNFT v1 · #122520 · protein
Crystal structure of the alanine racemase BSU17640 from bacillus subtilis
5IRP · Alanine racemase 2: “Crystal structure of the alanine racemase BSU17640 from bacillus subtilis”. X-ray diffraction, 4 ligands (UAH, MG, CL), 10 pockets (best druggability 0.80). MolNFT v1 #122520 on GenesisL1: 3D structure, binding…
- PDB
- 5IRP
- 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
- UAH, MG, CL, CO2
- Pockets
- 10 · best druggability 0.80
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
- UAH · (5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 20 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- CO2 · Carbon dioxide · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.80 | 0.94 | 55 | CL, UAH, TRS, CO2 |
| 2 | 293 | 0.78 | 0.90 | 48 | CL, MG |
| 3 | 271 | 0.75 | 0.88 | 54 | CL, CO2, UAH, TRS |
| 4 | 213 | 0.51 | 0.77 | 38 | empty |
| 5 | 121 | 0.47 | 0.79 | 26 | MG |
Interfaces
1 interface between chains.
- A–B · 3131 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5IRP · Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis · 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 A 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 5IRP · PDBe 5IRP · UniProt P94494
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