Research workbench
Crystal structure of histidinol-phosphate aminotransferase (ec 2.6.1.9) (imidazole acetol-phosphate transferase) (TM1040) from thermotoga maritima at 2.40 a resolution
Analyse Crystal structure of histidinol-phosphate aminotransferase (ec 2.6.1.9)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F8J
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol-phosphate aminotransferase
- EC
- 2.6.1.9
- UniProt
- Q9X0D0
- Ligands
- PMP
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 335 | 44% helix, 16% strand | Q9X0D0 |
| B, D | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 333 | 43% helix, 16% strand | Q9X0D0 |
| C | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 335 | 43% helix, 16% strand | Q9X0D0 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.75 | 0.95 | 27 | empty |
| 2 | 414 | 0.74 | 0.84 | 56 | PMP |
| 3 | 448 | 0.74 | 0.83 | 64 | PMP |
| 4 | 410 | 0.70 | 0.82 | 53 | PMP |
| 5 | 866 | 0.70 | 0.76 | 96 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 3299 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3221 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2F8J · Crystal structure of Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0D0 · AlphaFold monomer V2.0 prediction for histidinol-phosphate aminotransferase (Q9X0D0) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9X0D0
- Elsewhere: RCSB PDB 2F8J · PDBe 2F8J · UniProt Q9X0D0
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