Research workbench
Structure of NADP-dependent alcohol dehydrogenase
Analyse Structure of NADP-dependent alcohol dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KEV
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent alcohol dehydrogenase
- EC
- 1.1.1.2
- UniProt
- P25984
- Ligands
- NDP, ZN
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADP-dependent alcohol dehydrogenase (EC 1.1.1.2) | protein | 351 | 31% helix, 27% strand | P25984 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.80 | 0.82 | 103 | empty |
| 2 | 1085 | 0.80 | 0.81 | 103 | empty |
| 3 | 595 | 0.74 | 0.81 | 55 | NDP |
| 4 | 447 | 0.74 | 0.83 | 50 | NDP |
| 5 | 484 | 0.73 | 0.82 | 49 | NDP |
Interfaces
6 interfaces between chains.
- C–D · 1763 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1761 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1066 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1037 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 798 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1KEV · Structure of NADP-dependent alcohol dehydrogenase · the same entry in another collection · chain D against D, TM-score 1.00
- P25984 · AlphaFold monomer V2.0 prediction for NADP-dependent isopropanol dehydrogenase (P25984) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P25984
- Elsewhere: RCSB PDB 1KEV · PDBe 1KEV · UniProt P25984
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