Research workbench
Ternary complex crystal structure of secondary alcohol dehydrogenases from the thermoanaerobacter ethanolicus mutants C295 and I86A provides better understanding of catalytic mechanism
Analyse Ternary complex 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
- 7JNS
- Type
- protein
- Length
- 1,406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secondary-alcohol dehydrogenase
- EC
- 1.1.1.2
- UniProt
- P77990
- Ligands
- NAP, VF4, ZN, K
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secondary-alcohol dehydrogenase (EC 1.1.1.2) | protein | 350 | 31% helix, 25% strand | P77990 |
| B, C, D | Secondary-alcohol dehydrogenase (EC 1.1.1.2) | protein | 352 | 30% helix, 27% strand | P77990 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- VF4 · (1R,3S)-3-methylcyclohexan-1-ol · ligand · 3 copies · chains A, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- K · Potassium 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
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.75 | 0.79 | 75 | K |
| 2 | 714 | 0.74 | 0.80 | 60 | empty |
| 3 | 484 | 0.72 | 0.81 | 53 | NAP, VF4 |
| 4 | 817 | 0.71 | 0.77 | 106 | empty |
| 5 | 490 | 0.71 | 0.80 | 52 | NAP, VF4 |
Interfaces
6 interfaces between chains.
- C–D · 1895 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 1864 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1180 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1137 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 745 Ų buried · 10 hydrogen bonds · protein-protein
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 P77990
- Elsewhere: RCSB PDB 7JNS · PDBe 7JNS · UniProt P77990
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