MolNFT v1 · #148316 · protein
Crystal structure of the aspartate aminotranferase from rhizobium meliloti
6F35 · Aspartate aminotransferase B: “Crystal structure of the aspartate aminotranferase from rhizobium meliloti”. X-ray diffraction, 1 ligand (PLP), 3 pockets (best druggability 0.73). MolNFT v1 #148316 on GenesisL1: 3D structure, binding…
- PDB
- 6F35
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase B
- EC
- 2.6.1.1
- UniProt
- P58350
- Ligands
- PLP
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate aminotransferase B (EC 2.6.1.1) | protein | 400 | 46% helix, 15% strand | P58350 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.73 | 0.81 | 57 | PLP, ACT |
| 2 | 530 | 0.72 | 0.81 | 49 | PLP, ACT |
| 3 | 52 | 0.25 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2694 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6F35 · Crystal structure of the aspartate aminotranferase from Rhizobium meliloti · the same entry in another collection · chain A against A, TM-score 1.00
- P58350 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase (P58350) · a predicted model of the same protein · chain B 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 P58350
- Elsewhere: RCSB PDB 6F35 · PDBe 6F35 · UniProt P58350
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.