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
- 2YKU
- Type
- protein
- Length
- 1,295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-transaminase
- UniProt
- A3EYF7
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-transaminase | protein | 433 | 47% helix, 17% strand | A3EYF7 |
| B | Beta-transaminase | protein | 430 | 48% helix, 17% strand | A3EYF7 |
| C | Beta-transaminase | protein | 432 | 47% helix, 17% strand | A3EYF7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.79 | 0.99 | 42 | empty |
| 2 | 649 | 0.73 | 0.80 | 68 | PLP, EDO |
| 3 | 687 | 0.73 | 0.79 | 67 | PLP, EDO |
| 4 | 507 | 0.70 | 0.80 | 46 | EDO |
| 5 | 495 | 0.65 | 0.77 | 65 | PLP |
Interfaces
3 interfaces between chains.
- A–B · 4515 Ų buried · 62 hydrogen bonds · protein-protein
- B–C · 375 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2YKU · 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 2YKU · PDBe 2YKU · UniProt A3EYF7
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