Research workbench
Crystal structure of Ku80 and Sir4
Analyse Crystal structure of Ku80 and Sir4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y59
- Type
- protein
- Length
- 200 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.402
- Source
- Saccharomyces cerevisiae; Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- ATP-dependent DNA helicase II subunit 2; Sir4p
- EC
- 3.6.4.12
- UniProt
- Q04437, E7QD18
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · resolution 2.402 · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ATP-dependent DNA helicase II subunit 2 (EC 3.6.4.12) | protein | 188 | 40% helix, 22% strand | Q04437 |
| C | Sir4p | protein | 12 | 83% helix, 0% strand | E7QD18 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.46 | 0.77 | 23 | empty |
| 2 | 50 | 0.36 | 0.80 | 11 | empty |
Interfaces
1 interface between chains.
- B–C · 624 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 Q04437
- Every structure of UniProt E7QD18
- Elsewhere: RCSB PDB 5Y59 · PDBe 5Y59 · UniProt Q04437 · UniProt E7QD18
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