Research workbench
Yeast Ddi2 Cyanamide Hydratase
Analyse Yeast Ddi2 Cyanamide Hydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DKA
- Type
- protein
- Length
- 2,063 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.901
- Source
- Saccharomyces cerevisiae (strain YJM789)
- Molecule
- DNA damage-inducible protein
- UniProt
- A7A1Y4
- Ligands
- CNN, ZN, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.901 · 6 distinct chains · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA damage-inducible protein | protein | 230 | 62% helix, 2% strand | A7A1Y4 |
| D, G | DNA damage-inducible protein | protein | 229 | 62% helix, 2% strand | A7A1Y4 |
| E | DNA damage-inducible protein | protein | 230 | 62% helix, 2% strand | A7A1Y4 |
| F | DNA damage-inducible protein | protein | 232 | 62% helix, 3% strand | A7A1Y4 |
| H | DNA damage-inducible protein | protein | 227 | 62% helix, 2% strand | A7A1Y4 |
| I | DNA damage-inducible protein | protein | 226 | 62% helix, 2% strand | A7A1Y4 |
Ligands and binding sites
- CNN · Cyanamide · ligand · 7 copies · chains A, B, C, D, E, F, G
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
- SO4 · Sulfate ion · ion · 26 copies · chains A, B, C, E, D, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.82 | 0.83 | 128 | SO4 |
| 2 | 773 | 0.80 | 0.83 | 104 | SO4 |
| 3 | 414 | 0.72 | 0.83 | 58 | empty |
| 4 | 263 | 0.69 | 0.85 | 44 | SO4 |
| 5 | 259 | 0.67 | 0.83 | 44 | empty |
Interfaces
18 interfaces between chains.
- H–I · 1504 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1435 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1412 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1395 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 747 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DKA · Yeast DDI2 cyanamide hydratase · 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 A7A1Y4
- Elsewhere: RCSB PDB 6DKA · PDBe 6DKA · UniProt A7A1Y4
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