MolNFT v1 · #56266 · protein
Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine
2Z9X · Aspartate aminotransferase: “Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine”. X-ray diffraction, 4 ligands (ALA, PXL, SO4), 4 pockets (best druggability 0.73). MolNFT v1 #56266 on…
- PDB
- 2Z9X
- 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
- ALA, PXL, SO4, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate aminotransferase (EC 2.6.1.30) | protein | 392 | 45% helix, 15% strand | Q988B8 |
Ligands and binding sites
- ALA · Alanine · ligand · 2 copies · chains A, B
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.73 | 0.82 | 72 | ALA, PXL, GOL |
| 2 | 509 | 0.73 | 0.82 | 70 | ALA, PXL, GOL |
| 3 | 161 | 0.46 | 0.76 | 24 | empty |
| 4 | 58 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2123 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2Z9X · Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with… · the same entry in another collection · chain B against B, 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 2Z9X · PDBe 2Z9X · UniProt Q988B8
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