MolNFT v1 · #66008 · protein
Crystal structure of a histidinol-phosphate aminotransferase from geobacter metallireducens
3HDO: “Crystal structure of a histidinol-phosphate aminotransferase from geobacter metallireducens”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.81). MolNFT v1 #66008 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3HDO
- Type
- protein
- Length
- 699 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol-phosphate aminotransferase
- EC
- 2.6.1.9
- UniProt
- Q39YP6
- Ligands
- MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 350 | 41% helix, 15% strand | Q39YP6 |
| B | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 349 | 41% helix, 15% strand | Q39YP6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.81 | 0.97 | 27 | empty |
| 2 | 579 | 0.74 | 0.81 | 80 | GOL |
| 3 | 536 | 0.73 | 0.81 | 71 | empty |
| 4 | 68 | 0.30 | 0.73 | 19 | empty |
| 5 | 55 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2923 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3HDO · Crystal Structure of a Histidinol-phosphate aminotransferase from Geobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- Q39YP6 · AlphaFold monomer V2.0 prediction for histidinol-phosphate aminotransferase (Q39YP6) · a predicted model of the same protein · chain B 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 Q39YP6
- Elsewhere: RCSB PDB 3HDO · PDBe 3HDO · UniProt Q39YP6
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