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
- 3ZRR
- Type
- protein
- Length
- 758 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
- PXG, CA
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine-pyruvate aminotransferase (agxt) (EC 2.6.1.51) | protein | 379 | 43% helix, 16% strand | Q97VM5 |
Ligands and binding sites
- PXG · 3-[O-phosphonopyridoxyl]--amino-benzoic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.70 | 0.87 | 41 | PXG |
| 2 | 220 | 0.69 | 0.86 | 40 | PXG |
| 3 | 58 | 0.68 | 0.96 | 17 | empty |
| 4 | 59 | 0.66 | 0.95 | 16 | empty |
| 5 | 83 | 0.53 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2245 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3ZRR · 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 3ZRR · PDBe 3ZRR · UniProt Q97VM5
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