MolNFT v1 · #117238 · protein
Crystal structure of branched-chain aminotransferase from thermophilic archaea geoglobus acetivorans complexed with alpha-ketoglutarate
5E25: “Crystal structure of branched-chain aminotransferase from thermophilic archaea geoglobus acetivorans…”. X-ray diffraction, 2 ligands (PLP, AKG), 11 pockets (best druggability 0.76). MolNFT v1 #117238 on GenesisL1: 3D structure…
- PDB
- 5E25
- Type
- protein
- Length
- 864 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched-chain aminotransferase
- UniProt
- A0A0A7GJ30
- Ligands
- PLP, AKG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain aminotransferase | protein | 290 | 30% helix, 29% strand | A0A0A7GJ30 |
| B | Branched-chain aminotransferase | protein | 289 | 30% helix, 28% strand | A0A0A7GJ30 |
| C | Branched-chain aminotransferase | protein | 285 | 31% helix, 29% strand | A0A0A7GJ30 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- AKG · 2-oxoglutaric acid · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.76 | 0.92 | 41 | PLP, AKG |
| 2 | 350 | 0.70 | 0.83 | 49 | PLP |
| 3 | 308 | 0.63 | 0.80 | 33 | empty |
| 4 | 322 | 0.62 | 0.79 | 53 | PLP |
| 5 | 88 | 0.59 | 0.88 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2510 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 711 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 696 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5E25 · Crystal structure of branched-chain aminotransferase from thermophilic archaea Geoglobus… · 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 A0A0A7GJ30
- Elsewhere: RCSB PDB 5E25 · PDBe 5E25 · UniProt A0A0A7GJ30
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