Research workbench
Crystal structure of alanine-pyruvate aminotransferase with 2- methylserine
Analyse Crystal structure of alanine-pyruvate aminotransferase with 2- methylserine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YRI
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase, class V
- EC
- 2.6.-.-
- UniProt
- Q5SLX0
- Ligands
- MMM, PMP
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminotransferase, class V (EC 2.6.-.-) | protein | 352 | 44% helix, 16% strand | Q5SLX0 |
Ligands and binding sites
- MMM · (S,E)-3-hydroxy-2-((3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl)methyleneamino)-2-methylpropanoic acid · ligand · chains A, B
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.70 | 0.84 | 41 | PMP |
| 2 | 271 | 0.69 | 0.84 | 42 | MMM |
Interfaces
1 interface between chains.
- A–B · 1980 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2YRI · Crystal structure of alanine-pyruvate aminotransferase with 2-methylserine · the same entry in another collection · 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 Q5SLX0
- Elsewhere: RCSB PDB 2YRI · PDBe 2YRI · UniProt Q5SLX0
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