Research workbench
Structure of broad spectrum racemase from aeromonas hydrophila
Analyse Structure of broad spectrum racemase from aeromonas hydrophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BF5
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- A0KLG5
- Ligands
- PLP, NI, CL
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine racemase (EC 5.1.1.1) | protein | 396 | 34% helix, 24% strand | A0KLG5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains B
- CL · Chloride ion · ion · 23 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.82 | 0.94 | 33 | CL, GOL |
| 2 | 532 | 0.75 | 0.83 | 71 | PLP, CL |
| 3 | 349 | 0.75 | 0.86 | 36 | CL, GOL |
| 4 | 379 | 0.75 | 0.85 | 47 | PLP |
| 5 | 72 | 0.48 | 0.84 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 3855 Ų buried · 73 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 4BF5 · Structure of broad spectrum racemase from Aeromonas hydrophila · the same entry in another collection · chain A against A, TM-score 1.00
- A0KLG5 · AlphaFold monomer V2.0 prediction for broad specificity amino-acid racemase (A0KLG5) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 A0KLG5
- Elsewhere: RCSB PDB 4BF5 · PDBe 4BF5 · UniProt A0KLG5
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