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Crystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus with NADP and transition-state analogue inhibitor DMSO
Analyse Crystal structure of secondary alcohol dehydrogenases from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UTC
- Type
- protein
- Length
- 1,408 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Thermoanaerobacter pseudethanolicus
- Molecule
- Secondary-alcohol dehydrogenase
- EC
- 1.1.1.80
- UniProt
- P14941
- Ligands
- NAP, ZN
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.85 · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Secondary-alcohol dehydrogenase (EC 1.1.1.80) | protein | 352 | 30% helix, 27% strand | P14941 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 35 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.76 | 0.79 | 76 | DMS |
| 2 | 743 | 0.74 | 0.80 | 79 | DMS |
| 3 | 408 | 0.71 | 0.82 | 50 | NAP, DMS |
| 4 | 402 | 0.69 | 0.81 | 47 | NAP, DMS |
| 5 | 398 | 0.69 | 0.81 | 50 | NAP, DMS |
Interfaces
6 interfaces between chains.
- A–B · 1932 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1911 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1122 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1114 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 754 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7UTC · Crystal structure of secondary alcohol dehydrogenases from the thermoanaerobacter… · the same entry in another collection · chain D against D, TM-score 1.00
- P14941 · AlphaFold monomer V2.0 prediction for NADP-dependent isopropanol dehydrogenase (P14941) · a predicted model of the same protein · chain D 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 P14941
- Elsewhere: RCSB PDB 7UTC · PDBe 7UTC · UniProt P14941
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