MolNFT v1 · #178855 · protein
Ternary complex crystal structure of secondary alcohol dehydrogenases from the thermoanaerobacter ethanolicus mutants C295 and I86A provides better understanding of catalytic mechanism
7JNS · Secondary-alcohol dehydrogenase: “Ternary complex crystal structure of secondary alcohol dehydrogenases from the thermoanaerobacter ethanolicus…”. X-ray diffraction, 4 ligands (NAP, VF4, ZN), 12 pockets (best druggability 0.75).…
- 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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