Research workbench
2.2A resolution structure of cobalt and zinc bound thermostable alcohol dehydrogenase from pyrobaculum aerophilum
Analyse 2.2A resolution structure of cobalt and zinc bound thermostable alcohol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JBH
- Type
- protein
- Length
- 1,327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase (zinc)
- EC
- 1.1.1.1
- UniProt
- Q8ZUP0
- Ligands
- ZN, CO, CL
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alcohol dehydrogenase (zinc) (EC 1.1.1.1) | protein | 333 | 33% helix, 27% strand | Q8ZUP0 |
| B | Alcohol dehydrogenase (zinc) (EC 1.1.1.1) | protein | 329 | 31% helix, 28% strand | Q8ZUP0 |
| D | Alcohol dehydrogenase (zinc) (EC 1.1.1.1) | protein | 332 | 32% helix, 27% strand | Q8ZUP0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.66 | 0.79 | 58 | CL |
| 2 | 358 | 0.66 | 0.80 | 50 | empty |
| 3 | 402 | 0.65 | 0.79 | 50 | CL |
| 4 | 605 | 0.64 | 0.75 | 56 | empty |
| 5 | 391 | 0.61 | 0.77 | 42 | CL |
Interfaces
4 interfaces between chains.
- A–C · 708 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 428 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JBH · 2.2A resolution structure of cobalt and zinc bound thermostable alcohol dehydrogenase… · 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 Q8ZUP0
- Elsewhere: RCSB PDB 4JBH · PDBe 4JBH · UniProt Q8ZUP0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.