MolNFT v1 · #2052 · protein
Aspartate aminotransferase from thermus thermophilus with maleate
1BKG: “Aspartate aminotransferase from thermus thermophilus with maleate”. X-ray diffraction, 2 ligands (PMP, MAE), 14 pockets (best druggability 0.83). MolNFT v1 #2052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1BKG
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- Q56232
- Ligands
- PMP, MAE
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aspartate aminotransferase (EC 2.6.1.1) | protein | 382 | 47% helix, 15% strand | Q56232 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- MAE · Maleic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.83 | 0.84 | 128 | empty |
| 2 | 424 | 0.73 | 0.83 | 46 | PMP, MAE |
| 3 | 540 | 0.73 | 0.82 | 71 | PMP, MAE |
| 4 | 587 | 0.72 | 0.80 | 70 | PMP, MAE |
| 5 | 565 | 0.72 | 0.80 | 69 | PMP, MAE |
Interfaces
6 interfaces between chains.
- A–B · 3204 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 3195 Ų buried · 72 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 338 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 51 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1BKG · Aspartate aminotransferase from thermus thermophilus with maleate · the same entry in another collection · chain D against D, TM-score 1.00
- Q56232 · AlphaFold monomer V2.0 prediction for ASPARTATE/PREPHENATE aminotransferase (Q56232) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q56232
- Elsewhere: RCSB PDB 1BKG · PDBe 1BKG · UniProt Q56232
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