Research workbench
Alanine aminotransferase from pyrococcus furiosus pfu-1397077-001
Analyse Alanine aminotransferase from pyrococcus furiosus pfu-1397077-001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XI9
- Type
- protein
- Length
- 1,553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transaminase
- UniProt
- Q9P9M8
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative transaminase | protein | 388 | 46% helix, 16% strand | Q9P9M8 |
| B, D | Putative transaminase | protein | 386 | 45% helix, 16% strand | Q9P9M8 |
| C | Putative transaminase | protein | 393 | 47% helix, 16% strand | Q9P9M8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.84 | 0.97 | 35 | empty |
| 2 | 207 | 0.83 | 0.96 | 34 | empty |
| 3 | 993 | 0.76 | 0.79 | 96 | empty |
| 4 | 438 | 0.72 | 0.82 | 38 | empty |
| 5 | 60 | 0.69 | 0.95 | 19 | PLP |
Interfaces
5 interfaces between chains.
- C–D · 2752 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2720 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 132 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1XI9 · Alanine aminotransferase from Pyrococcus furiosus Pfu-1397077-001 · 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 Q9P9M8
- Elsewhere: RCSB PDB 1XI9 · PDBe 1XI9 · UniProt Q9P9M8
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