Research workbench
Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme
Analyse Symmetry in Yeast Alcohol Dehydrogenase 1 -Open Form of Apoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCQ
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Saccharomyces cerevisiae
- Molecule
- Alcohol dehydrogenase
- EC
- 1.1.1.1
- UniProt
- S5RZC2
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 3.2 · 1 distinct chain · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 347 | 28% helix, 28% strand | S5RZC2 |
Ligands and binding sites
- 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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.80 | 0.96 | 28 | empty |
| 2 | 159 | 0.78 | 0.95 | 28 | empty |
| 3 | 541 | 0.72 | 0.81 | 95 | empty |
| 4 | 460 | 0.70 | 0.80 | 56 | empty |
| 5 | 438 | 0.70 | 0.80 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1618 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1618 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 949 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 949 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 515 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7KCQ · Symmetry in yeast alcohol dehydrogenase 1 -open form of apoenzyme · 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 S5RZC2
- Elsewhere: RCSB PDB 7KCQ · PDBe 7KCQ · UniProt S5RZC2
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