Research workbench
Structural determinants of the beta-selectivity of a bacterial aminotransferase
Analyse Structural determinants of the beta-selectivity of a bacterial aminotransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YKX
- Type
- protein
- Length
- 1,289 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-transaminase
- UniProt
- A3EYF7
- Ligands
- PLP, AKG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-transaminase | protein | 431 | 47% helix, 17% strand | A3EYF7 |
| B, C | Beta-transaminase | protein | 429 | 48% helix, 17% strand | A3EYF7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 40 | empty |
| 2 | 717 | 0.72 | 0.79 | 64 | PLP, AKG |
| 3 | 682 | 0.72 | 0.79 | 64 | PLP, AKG |
| 4 | 775 | 0.70 | 0.76 | 87 | PLP, AKG |
| 5 | 471 | 0.68 | 0.79 | 49 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 4478 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2YKX · Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase · 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 A3EYF7
- Elsewhere: RCSB PDB 2YKX · PDBe 2YKX · UniProt A3EYF7
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