Research workbench
Joint X-RAY/NEUTRON structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5
Analyse Joint X-RAY/NEUTRON structure of aspartate aminotransferase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJZ
- Type
- protein
- Length
- 824 residues
- Chains
- 2
- Method
- neutron diffraction; x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase, cytoplasmic
- EC
- 2.6.1.1, 2.6.1.3
- UniProt
- P00503
- Ligands
- PLA
- Pockets
- 11 · best druggability 0.72
Structure
neutron diffraction; x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1, 2.6.1.3) | protein | 412 | 46% helix, 13% strand | P00503 |
Ligands and binding sites
- PLA · 2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-amino]-2-methyl-succinic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.72 | 0.78 | 65 | empty |
| 2 | 96 | 0.69 | 0.93 | 25 | empty |
| 3 | 296 | 0.69 | 0.84 | 52 | PLA |
| 4 | 152 | 0.55 | 0.81 | 24 | empty |
| 5 | 170 | 0.55 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3578 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 5VJZ · Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate… · the same entry in another collection · chain A against A, TM-score 1.00
- P00503 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase, cytoplasmic (P00503) · 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 P00503
- Elsewhere: RCSB PDB 5VJZ · PDBe 5VJZ · UniProt P00503
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