Research workbench
Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine
Analyse Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z9V
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.30
- UniProt
- Q988B8
- Ligands
- PXM, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate aminotransferase (EC 2.6.1.30) | protein | 392 | 45% helix, 14% strand | Q988B8 |
Ligands and binding sites
- PXM · 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.68 | 0.83 | 38 | SO4, PXM, GOL |
| 2 | 296 | 0.68 | 0.83 | 41 | SO4, PXM, GOL |
| 3 | 227 | 0.55 | 0.78 | 29 | empty |
| 4 | 165 | 0.49 | 0.77 | 28 | empty |
| 5 | 170 | 0.47 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2126 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2Z9V · Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine · the same entry in another collection · chain A against A, TM-score 1.00
- Q988B8 · AlphaFold monomer V2.0 prediction for pyridoxamine--pyruvate transaminase (Q988B8) · a predicted model of the same protein · 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 Q988B8
- Elsewhere: RCSB PDB 2Z9V · PDBe 2Z9V · UniProt Q988B8
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