Research workbench
Crystal structure and substrate specificity of a thermophilic archaeal serine : pyruvate aminotransferase from sulfolobus solfataricus
Analyse Crystal structure and substrate specificity of a thermophilic archaeal serine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZRQ
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine-pyruvate aminotransferase (agxt)
- EC
- 2.6.1.51
- UniProt
- Q97VM5
- Ligands
- PMP
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine-pyruvate aminotransferase (agxt) (EC 2.6.1.51) | protein | 382 | 43% helix, 17% strand | Q97VM5 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.59 | 0.80 | 44 | PMP |
| 2 | 145 | 0.59 | 0.84 | 35 | PMP |
| 3 | 55 | 0.33 | 0.77 | 13 | empty |
| 4 | 66 | 0.31 | 0.75 | 15 | empty |
| 5 | 64 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2118 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3ZRQ · Crystal structure and substrate specificity of a thermophilic archaeal serine : pyruvate… · 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 Q97VM5
- Elsewhere: RCSB PDB 3ZRQ · PDBe 3ZRQ · UniProt Q97VM5
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