MolNFT v1 · #118716 · protein
Alanine racemase from streptomyces coelicolor A3(2) with bound propionate inhibitor
5FAG: “Alanine racemase from streptomyces coelicolor A3(2) with bound propionate inhibitor”. X-ray diffraction, 3 ligands (PLP, NA, NO3), 18 pockets (best druggability 0.77). MolNFT v1 #118716 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FAG
- Type
- protein
- Length
- 1,536 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, NA, NO3
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 390 | 36% helix, 22% strand | O86786 |
| B, C, D | Alanine racemase (EC 5.1.1.1) | protein | 382 | 35% helix, 23% strand | O86786 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C
- NO3 · Nitrate ion · ion · 2 copies · chains A, C, B
- PPI · Propanoic acid · additive · 8 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 | 242 | 0.77 | 0.90 | 56 | PLP, PPI |
| 2 | 197 | 0.74 | 0.90 | 46 | PLP, PPI |
| 3 | 201 | 0.74 | 0.89 | 43 | PPI, PLP |
| 4 | 197 | 0.73 | 0.89 | 42 | PPI, PLP |
| 5 | 55 | 0.72 | 0.99 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3185 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3172 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 373 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 modified (pyridoxal phosphate Schiff base, carboxylation).
Compared structures
- 5FAG · Alanine Racemase from Streptomyces coelicolor A3(2) with Bound Propionate Inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- O86786 · AlphaFold monomer V2.0 prediction for alanine racemase (O86786) · a predicted model of the same protein · chain D 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 O86786
- Elsewhere: RCSB PDB 5FAG · PDBe 5FAG · UniProt O86786
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