MolNFT v1 · #137703 · protein
E.COLI aspartate aminotransferase-(1R,3S,4S)-3-amino-4- fluorocyclopentane-1-carboxylic acid (fcp)
5VWQ: “E.COLI aspartate aminotransferase-(1R,3S,4S)-3-amino-4- fluorocyclopentane-1-carboxylic acid (fcp)”. X-ray diffraction, 1 ligand (PMP), 19 pockets (best druggability 0.74). MolNFT v1 #137703 on GenesisL1: 3D structure, binding sites…
- PDB
- 5VWQ
- Type
- protein
- Length
- 1,584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P00509
- Ligands
- PMP
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Aspartate aminotransferase (EC 2.6.1.1) | protein | 396 | 48% helix, 14% strand | P00509 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.74 | 0.80 | 67 | PMP |
| 2 | 762 | 0.74 | 0.79 | 80 | PMP |
| 3 | 618 | 0.70 | 0.78 | 50 | empty |
| 4 | 624 | 0.68 | 0.77 | 51 | empty |
| 5 | 293 | 0.60 | 0.78 | 49 | PMP |
Interfaces
4 interfaces between chains.
- A–D · 3150 Ų buried · 60 hydrogen bonds · protein-protein
- A–J · 337 Ų buried · 0 hydrogen bonds · protein-protein
- D–G · 331 Ų buried · 0 hydrogen bonds · protein-protein
- G–J · 158 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5VWQ · E.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic… · the same entry in another collection · chain J against J, TM-score 1.00
- P00509 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase (P00509) · a predicted model of the same protein · chain J 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 P00509
- Elsewhere: RCSB PDB 5VWQ · PDBe 5VWQ · UniProt P00509
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