MolNFT v1 · #8878 · protein
Three-dimensional structures of three human alcohol dehydrogenase variants: correlations with their functional differences
1HDY: “Three-dimensional structures of three human alcohol dehydrogenase variants: correlations with their…”. X-ray diffraction, 4 ligands (NAD, PYZ, ZN), 6 pockets (best druggability 0.74). MolNFT v1 #8878 on GenesisL1: 3D structure…
- PDB
- 1HDY
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- P00325
- Ligands
- NAD, PYZ, ZN, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 374 | 30% helix, 26% strand | P00325 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PYZ · 4-iodopyrazole · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.74 | 0.82 | 69 | ZN, NAD, PYZ |
| 2 | 438 | 0.74 | 0.83 | 60 | NAD, PYZ |
| 3 | 514 | 0.69 | 0.80 | 54 | empty |
| 4 | 67 | 0.49 | 0.85 | 21 | empty |
| 5 | 62 | 0.45 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1779 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1HDY · Three-dimensional structures of three human alcohol dehydrogenase variants: correlations… · the same entry in another collection · chain A against A, TM-score 1.00
- P00325 · AlphaFold monomer V2.0 prediction for all-trans-retinol dehydrogenase [NAD(+)] ADH1B… · a predicted model of the same protein · 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 P00325
- Elsewhere: RCSB PDB 1HDY · PDBe 1HDY · UniProt P00325
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