Research workbench
E.COLI aspartate aminotransferase-(1R,3S,4S)-3-amino-4- fluorocyclopentane-1-carboxylic acid (fcp)-alpha-ketoglutarate
Analyse E.COLI aspartate aminotransferase-(1R,3S,4S)-3-amino-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VWR
- Type
- protein
- Length
- 396 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P00509
- Ligands
- PL6
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase (EC 2.6.1.1) | protein | 396 | 46% helix, 14% strand | P00509 |
Ligands and binding sites
- PL6 · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.65 | 0.84 | 32 | PL6 |
| 2 | 97 | 0.38 | 0.76 | 25 | empty |
| 3 | 58 | 0.38 | 0.80 | 14 | empty |
| 4 | 87 | 0.36 | 0.75 | 23 | empty |
| 5 | 52 | 0.34 | 0.78 | 14 | empty |
Compared structures
- 5VWR · E.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic… · the same entry in another collection · chain A against A, TM-score 1.00
- P00509 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase (P00509) · a predicted model of the same protein · chain A 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 5VWR · PDBe 5VWR · UniProt P00509
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