Research workbench
Crystal structure of R. ruber adh-a, mutant Y294F, W295A
Analyse Crystal structure of R. ruber adh-a, mutant Y294F, W295A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O8Q
- Type
- protein
- Length
- 2,760 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- UniProt
- A0A1Q8I6M1
- Ligands
- NAD, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Alcohol dehydrogenase | protein | 345 | 29% helix, 25% strand | A0A1Q8I6M1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, E, B, H, C, F, D, G
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.82 | 0.84 | 142 | empty |
| 2 | 870 | 0.76 | 0.79 | 75 | ZN, NAD |
| 3 | 872 | 0.76 | 0.79 | 72 | ZN, NAD |
| 4 | 830 | 0.76 | 0.79 | 69 | NAD |
| 5 | 868 | 0.76 | 0.79 | 72 | NAD |
Interfaces
14 interfaces between chains.
- D–G · 1463 Ų buried · 17 hydrogen bonds · protein-protein
- B–H · 1425 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1421 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 1411 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 657 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5O8Q · Crystal structure of R. ruber ADH-A, mutant Y294F, W295A · the same entry in another collection · chain A 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 A0A1Q8I6M1
- Elsewhere: RCSB PDB 5O8Q · PDBe 5O8Q · UniProt A0A1Q8I6M1
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