MolNFT v1 · #129193 · protein
Crystal structure of R. ruber adh-a, mutant Y54G, L119Y
5OD3 · Alcohol dehydrogenase: “Crystal structure of R. ruber adh-a, mutant Y54G, L119Y”. X-ray diffraction, 2 ligands (NAD, ZN), 12 pockets (best druggability 0.81). MolNFT v1 #129193 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5OD3
- Type
- protein
- Length
- 1,381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- UniProt
- A0A1Q8I6M1
- Ligands
- NAD, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alcohol dehydrogenase | protein | 346 | 30% helix, 25% strand | A0A1Q8I6M1 |
| B, C, D | Alcohol dehydrogenase | protein | 345 | 30% helix, 25% strand | A0A1Q8I6M1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- 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
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.81 | 0.84 | 119 | empty |
| 2 | 829 | 0.78 | 0.81 | 75 | NAD |
| 3 | 770 | 0.78 | 0.82 | 74 | NAD |
| 4 | 772 | 0.77 | 0.81 | 76 | NAD |
| 5 | 757 | 0.77 | 0.81 | 76 | NAD |
Interfaces
6 interfaces between chains.
- B–C · 1451 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1436 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 522 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 463 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5OD3 · Crystal structure of R. ruber ADH-A, mutant Y54G, L119Y · the same entry in another collection · chain B against B, 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 5OD3 · PDBe 5OD3 · UniProt A0A1Q8I6M1
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