MolNFT v1 · #25160 · protein
Crystal structure of an iron containing alcohol dehydrogenase
1VHD · Alcohol dehydrogenase, iron-containing: “Crystal structure of an iron containing alcohol dehydrogenase”. X-ray diffraction, 2 ligands (NAP, ZN), 5 pockets (best druggability 0.77). MolNFT v1 #25160 on GenesisL1: 3D structure…
- PDB
- 1VHD
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase, iron-containing
- EC
- 1.1.1.-
- UniProt
- Q9X022
- Ligands
- NAP, ZN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alcohol dehydrogenase, iron-containing (EC 1.1.1.-) | protein | 361 | 57% helix, 14% strand | Q9X022 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.77 | 0.81 | 95 | NAP |
| 2 | 712 | 0.77 | 0.82 | 76 | NAP |
| 3 | 114 | 0.37 | 0.73 | 21 | empty |
| 4 | 104 | 0.35 | 0.73 | 18 | empty |
| 5 | 70 | 0.27 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1277 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 1VHD · Crystal structure of an iron containing alcohol dehydrogenase · 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 Q9X022
- Elsewhere: RCSB PDB 1VHD · PDBe 1VHD · UniProt Q9X022
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