MolNFT v1 · #12224 · protein
L-histidinol dehydrogenase (hisd) structure complexed with L- histidinol (substrate), zinc and NAD (cofactor)
1KAE: “L-histidinol dehydrogenase (hisd) structure complexed with L- histidinol (substrate), zinc and NAD (cofactor)”. X-ray diffraction, 4 ligands (NAD, HSO, ZN), 7 pockets (best druggability 0.85). MolNFT v1 #12224 on GenesisL1: 3D…
- PDB
- 1KAE
- Type
- protein
- Length
- 868 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol dehydrogenase
- EC
- 1.1.1.23
- UniProt
- P06988
- Ligands
- NAD, HSO, ZN, SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histidinol dehydrogenase (EC 1.1.1.23) | protein | 434 | 48% helix, 17% strand | P06988 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- HSO · L-histidinol · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
- IMD · Imidazole · additive · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.85 | 0.86 | 94 | empty |
| 2 | 323 | 0.73 | 0.86 | 38 | IMD |
| 3 | 254 | 0.70 | 0.86 | 42 | HSO |
| 4 | 150 | 0.62 | 0.85 | 21 | empty |
| 5 | 52 | 0.43 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 5201 Ų buried · 91 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 1KAE · L-histidinol dehydrogenase (hisd) structure complexed with L-histidinol (substrate), zinc… · the same entry in another collection · chain A against A, TM-score 1.00
- P06988 · AlphaFold monomer V2.0 prediction for histidinol dehydrogenase (P06988) · a predicted model of the same protein · chain A 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 P06988
- Elsewhere: RCSB PDB 1KAE · PDBe 1KAE · UniProt P06988
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