Research workbench
Crystal structure of mutant of ht- alcohol dehydrogenase with substrate analogue butyramide
Analyse Crystal structure of mutant of ht- alcohol dehydrogenase with substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PII
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- P42328
- Ligands
- BMD, ZN, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 337 | 31% helix, 28% strand | P42328 |
Ligands and binding sites
- BMD · Butyramide · ligand · 4 copies · chains A, D, C, B
- ZN · Zinc ion · metal · 8 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.73 | 0.77 | 108 | empty |
| 2 | 1010 | 0.73 | 0.76 | 110 | empty |
| 3 | 566 | 0.72 | 0.80 | 52 | empty |
| 4 | 611 | 0.71 | 0.79 | 68 | BMD, SO4 |
| 5 | 603 | 0.71 | 0.79 | 64 | BMD, SO4 |
Interfaces
6 interfaces between chains.
- A–D · 1772 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 1741 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 629 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 622 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 467 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3PII · Crystal structure of Mutant of ht- Alcohol Dehydrogenase with substrate analogue… · the same entry in another collection · chain D against D, TM-score 1.00
- P42328 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase (P42328) · a predicted model of the same protein · chain D 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 P42328
- Elsewhere: RCSB PDB 3PII · PDBe 3PII · UniProt P42328
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