Research workbench
Structure of putative alcohol dehydrogenase (TM_042) from thermotoga maritima
Analyse Structure of putative alcohol dehydrogenase (TM_042) from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IP1
- Type
- protein
- Length
- 1,583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase, zinc-containing
- UniProt
- Q9WYP3
- Ligands
- CD, CL
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Alcohol dehydrogenase, zinc-containing | protein | 396 | 30% helix, 28% strand | Q9WYP3 |
| C | Alcohol dehydrogenase, zinc-containing | protein | 395 | 30% helix, 27% strand | Q9WYP3 |
Ligands and binding sites
- CD · Cadmium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains B
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 | 687 | 0.82 | 0.86 | 98 | empty |
| 2 | 559 | 0.79 | 0.85 | 83 | empty |
| 3 | 971 | 0.78 | 0.80 | 69 | CD |
| 4 | 1073 | 0.77 | 0.79 | 75 | CD |
| 5 | 1148 | 0.77 | 0.79 | 76 | CD |
Interfaces
6 interfaces between chains.
- A–D · 1664 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1649 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 972 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 962 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3IP1 · Structure of putative alcohol dehydrogenase (TM_042) from Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYP3 · AlphaFold monomer V2.0 prediction for scyllo-inosose 3-dehydrogenase (Q9WYP3) · a predicted model of the same protein · 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 Q9WYP3
- Elsewhere: RCSB PDB 3IP1 · PDBe 3IP1 · UniProt Q9WYP3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.