MolNFT v1 · #161207 · protein
Crystal structure of the alanine racemase from bacillus subtilis in the presence of only peg 4000 and magnesium chloride in the crystallization condition
6Q72 · Alanine racemase 2: “Crystal structure of the alanine racemase from bacillus subtilis in the presence of only peg 4000 and…”. X-ray diffraction, 2 ligands (PLP, CL), 20 pockets (best druggability 0.77). MolNFT v1 #161207 on…
- PDB
- 6Q72
- Type
- protein
- Length
- 1,544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase 2
- UniProt
- A0A386RMP5
- Ligands
- PLP, CL
- Pockets
- 20 · 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, D, E | Alanine racemase 2 | protein | 386 | 34% helix, 26% strand | A0A386RMP5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, D, E
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.77 | 0.89 | 49 | empty |
| 2 | 327 | 0.76 | 0.88 | 52 | empty |
| 3 | 295 | 0.75 | 0.88 | 54 | PLP, CL |
| 4 | 274 | 0.75 | 0.88 | 59 | PLP, CL |
| 5 | 294 | 0.75 | 0.87 | 63 | PLP, CL |
Interfaces
4 interfaces between chains.
- D–E · 3072 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3068 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 730 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 682 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor, 4 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 6Q72 · Crystal structure of the alanine racemase from Bacillus subtilis in the presence of only… · 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 A0A386RMP5
- Elsewhere: RCSB PDB 6Q72 · PDBe 6Q72 · UniProt A0A386RMP5
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