MolNFT v1 · #12236 · protein
L-histidinol dehydrogenase (hisd) structure complexed with histamine (inhibitor), zinc and NAD (cofactor)
1KAR: “L-histidinol dehydrogenase (hisd) structure complexed with histamine (inhibitor), zinc and NAD (cofactor)”. X-ray diffraction, 2 ligands (HSM, ZN), 5 pockets (best druggability 0.87). MolNFT v1 #12236 on GenesisL1: 3D structure…
- PDB
- 1KAR
- Type
- protein
- Length
- 862 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
- HSM, ZN
- Pockets
- 5 · best druggability 0.87
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 | 431 | 48% helix, 17% strand | P06988 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.87 | 0.88 | 131 | HSM |
| 2 | 101 | 0.44 | 0.78 | 19 | empty |
| 3 | 87 | 0.44 | 0.79 | 17 | empty |
| 4 | 67 | 0.42 | 0.80 | 18 | empty |
| 5 | 50 | 0.34 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 5306 Ų buried · 92 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1KAR · L-histidinol dehydrogenase (hisd) structure complexed with histamine (inhibitor), zinc… · the same entry in another collection · chain B against B, 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 1KAR · PDBe 1KAR · UniProt P06988
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