MolNFT v1 · #108598 · protein
Crystal structure of histidinol-phosphate aminotransferase from sinorhizobium meliloti in complex with pyridoxal-5'-phosphate
4WBT · Probable histidinol-phosphate aminotransferase: “Crystal structure of histidinol-phosphate aminotransferase from sinorhizobium meliloti in complex with…”. X-ray diffraction, 1 ligand (PLP), 13 pockets (best druggability 0.66).…
- PDB
- 4WBT
- Type
- protein
- Length
- 1,104 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable histidinol-phosphate aminotransferase
- EC
- 2.6.1.9
- UniProt
- Q92R63
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 369 | 48% helix, 14% strand | Q92R63 |
| B | Probable histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 368 | 48% helix, 14% strand | Q92R63 |
| C | Probable histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 367 | 48% helix, 14% strand | Q92R63 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PGE · Triethylene glycol · additive · chains B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.66 | 0.77 | 51 | empty |
| 2 | 390 | 0.63 | 0.78 | 47 | PLP |
| 3 | 343 | 0.61 | 0.78 | 48 | PLP |
| 4 | 447 | 0.60 | 0.75 | 46 | empty |
| 5 | 401 | 0.59 | 0.76 | 38 | empty |
Interfaces
3 interfaces between chains.
- B–C · 292 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 262 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 177 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified, 3 cofactor (engineered, pyridoxal phosphate Schiff base, oxidation).
Compared structures
- 4WBT · Crystal structure of histidinol-phosphate aminotransferase from Sinorhizobium meliloti in… · 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 Q92R63
- Elsewhere: RCSB PDB 4WBT · PDBe 4WBT · UniProt Q92R63
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