MolNFT v1 · #129068 · protein
Crystal structure of R. ruber adh-a, mutant Y294F, W295A, Y54F, F43S, H39Y
5O9F · Alcohol dehydrogenase: “Crystal structure of R. ruber adh-a, mutant Y294F, W295A, Y54F, F43S, H39Y”. X-ray diffraction, 3 ligands (NAD, 9ON, ZN), 13 pockets (best druggability 0.76). MolNFT v1 #129068 on GenesisL1: 3D structure…
- PDB
- 5O9F
- Type
- protein
- Length
- 1,383 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- UniProt
- A0A1Q8I6M1
- Ligands
- NAD, 9ON, ZN
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Alcohol dehydrogenase | protein | 346 | 28% helix, 25% strand | A0A1Q8I6M1 |
| C | Alcohol dehydrogenase | protein | 345 | 28% helix, 25% strand | A0A1Q8I6M1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- 9ON · (2~{S})-2-methylpentanedioic acid · ligand · 3 copies · chains A, B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.76 | 0.83 | 92 | empty |
| 2 | 739 | 0.76 | 0.80 | 69 | NAD, 9ON |
| 3 | 805 | 0.75 | 0.79 | 69 | NAD |
| 4 | 825 | 0.75 | 0.79 | 77 | NAD, 9ON |
| 5 | 758 | 0.75 | 0.80 | 68 | NAD, 9ON |
Interfaces
6 interfaces between chains.
- B–C · 1527 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1487 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 508 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5O9F · Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43S, H39Y · 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 5O9F · PDBe 5O9F · UniProt A0A1Q8I6M1
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