Research workbench
Crystal structure of a putative histidinol dehydrogenase (target psi- 014034) from methylococcus capsulatus
Analyse Crystal structure of a putative histidinol dehydrogenase (target psi- 014034)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GIC
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol dehydrogenase
- EC
- 1.1.1.23
- UniProt
- Q606Q2
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidinol dehydrogenase (EC 1.1.1.23) | protein | 382 | 48% helix, 18% strand | Q606Q2 |
| B | Histidinol dehydrogenase (EC 1.1.1.23) | protein | 382 | 48% helix, 18% strand | Q606Q2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.86 | 0.88 | 86 | empty |
| 2 | 172 | 0.67 | 0.86 | 23 | empty |
| 3 | 216 | 0.65 | 0.84 | 25 | empty |
| 4 | 121 | 0.54 | 0.83 | 24 | empty |
| 5 | 105 | 0.51 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2502 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4GIC · Crystal Structure Of a Putative Histidinol dehydrogenase (Target PSI-014034) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q606Q2 · AlphaFold monomer V2.0 prediction for histidinol dehydrogenase (Q606Q2) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q606Q2
- Elsewhere: RCSB PDB 4GIC · PDBe 4GIC · UniProt Q606Q2
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