MolNFT v1 · #146534 · protein
Yeast DDI2 cyanamide hydratase
6DKD · DNA damage-inducible protein: “Yeast DDI2 cyanamide hydratase”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #146534 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DKD
- Type
- protein
- Length
- 2,057 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 0.80
Structure
x-ray diffraction · 5 distinct chains · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, G | DNA damage-inducible protein | protein | 229 | 62% helix, 2% strand | A7A1Y4 |
| B, C | DNA damage-inducible protein | protein | 230 | 63% helix, 2% strand | A7A1Y4 |
| F | DNA damage-inducible protein | protein | 230 | 62% helix, 2% strand | A7A1Y4 |
| H | DNA damage-inducible protein | protein | 225 | 63% helix, 2% strand | A7A1Y4 |
| I | DNA damage-inducible protein | protein | 226 | 63% 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 · 27 copies · chains A, B, C, E, D, G, F
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 | 825 | 0.80 | 0.83 | 114 | SO4 |
| 2 | 900 | 0.79 | 0.82 | 113 | SO4 |
| 3 | 428 | 0.71 | 0.82 | 57 | empty |
| 4 | 332 | 0.70 | 0.83 | 49 | SO4 |
| 5 | 281 | 0.69 | 0.84 | 43 | SO4 |
Interfaces
18 interfaces between chains.
- H–I · 1511 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1468 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1448 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1427 Ų buried · 18 hydrogen bonds · protein-protein
- F–H · 703 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DKD · 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 6DKD · PDBe 6DKD · UniProt A7A1Y4
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