Research workbench
Bacterial secondary alcohol dehydrogenase (apo-form)
Analyse Bacterial secondary alcohol dehydrogenase (apo-form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PED
- 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
- ZN
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADP-dependent alcohol dehydrogenase (EC 1.1.1.2) | protein | 351 | 32% helix, 26% strand | P25984 |
Ligands and binding sites
- 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
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.80 | 0.82 | 98 | empty |
| 2 | 1076 | 0.80 | 0.82 | 98 | empty |
| 3 | 465 | 0.72 | 0.82 | 49 | empty |
| 4 | 430 | 0.72 | 0.82 | 49 | empty |
| 5 | 431 | 0.72 | 0.82 | 50 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1780 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1708 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1086 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 804 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1PED · Bacterial secondary alcohol dehydrogenase (apo-form) · 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 1PED · PDBe 1PED · UniProt P25984
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