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
- 6DK9
- Type
- protein
- Length
- 2,059 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-inducible protein
- UniProt
- A7A1Y4
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G | DNA damage-inducible protein | protein | 229 | 62% helix, 2% strand | A7A1Y4 |
| F | DNA damage-inducible protein | protein | 232 | 61% helix, 2% strand | A7A1Y4 |
| H | DNA damage-inducible protein | protein | 227 | 60% helix, 3% strand | A7A1Y4 |
| I | DNA damage-inducible protein | protein | 226 | 62% helix, 2% strand | A7A1Y4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
- SO4 · Sulfate ion · ion · 28 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.73 | 0.85 | 55 | SO4 |
| 2 | 448 | 0.72 | 0.82 | 57 | empty |
| 3 | 390 | 0.72 | 0.83 | 55 | SO4 |
| 4 | 407 | 0.72 | 0.83 | 66 | SO4 |
| 5 | 305 | 0.71 | 0.84 | 49 | SO4 |
Interfaces
18 interfaces between chains.
- H–I · 1505 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1444 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1432 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1414 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 702 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DK9 · Yeast Ddi2 Cyanamide Hydratase · the same entry in another collection · chain E against E, 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 6DK9 · PDBe 6DK9 · UniProt A7A1Y4
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