MolNFT v1 · #118712 · protein
Alanine racemase from streptomyces coelicolor A3(2)
5FAC: “Alanine racemase from streptomyces coelicolor A3(2)”. X-ray diffraction, 2 ligands (PLP, CL), 18 pockets (best druggability 0.72). MolNFT v1 #118712 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FAC
- Type
- protein
- Length
- 1,529 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- O86786
- Ligands
- PLP, CL
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 384 | 35% helix, 23% strand | O86786 |
| B, D | Alanine racemase (EC 5.1.1.1) | protein | 381 | 35% helix, 23% strand | O86786 |
| C | Alanine racemase (EC 5.1.1.1) | protein | 383 | 35% helix, 23% strand | O86786 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.72 | 0.89 | 43 | PLP |
| 2 | 170 | 0.72 | 0.90 | 41 | PLP |
| 3 | 233 | 0.71 | 0.87 | 43 | PLP |
| 4 | 53 | 0.71 | 0.98 | 17 | empty |
| 5 | 165 | 0.70 | 0.89 | 42 | PLP |
Interfaces
3 interfaces between chains.
- C–D · 3243 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3206 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 344 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified (pyridoxal phosphate Schiff base, carboxylation).
Compared structures
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 O86786
- Elsewhere: RCSB PDB 5FAC · PDBe 5FAC · UniProt O86786
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