MolNFT v1 · #115245 · protein
I220V horse liver alcohol dehydrogenase complexed with NAD and pyrazole
5CDU · Alcohol dehydrogenase E chain: “I220V horse liver alcohol dehydrogenase complexed with NAD and pyrazole”. X-ray diffraction, 3 ligands (NAJ, PZO, ZN), 4 pockets (best druggability 0.73). MolNFT v1 #115245 on GenesisL1: 3D structure…
- PDB
- 5CDU
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase E chain
- EC
- 1.1.1.1
- UniProt
- P00327
- Ligands
- NAJ, PZO, ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alcohol dehydrogenase E chain (EC 1.1.1.1) | protein | 374 | 30% helix, 26% strand | P00327 |
Ligands and binding sites
- NAJ · Nicotinamide-adenine-dinucleotide (acidic form) · ligand · 2 copies · chains A, B
- PZO · Pyrazole · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.73 | 0.84 | 47 | NAJ, PZO |
| 2 | 580 | 0.73 | 0.80 | 78 | NAJ, PZO |
| 3 | 386 | 0.66 | 0.80 | 45 | empty |
| 4 | 149 | 0.48 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1769 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- P00327 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase E chain (P00327) · a predicted model of the same protein · chain B 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 P00327
- Elsewhere: RCSB PDB 5CDU · PDBe 5CDU · UniProt P00327
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