Research workbench
Crystal structures of holliday junction resolvases from archaeoglobus fulgidus bound to DNA substrate
Analyse Crystal structures of holliday junction resolvases from archaeoglobus fulgidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WIW
- Type
- protein + DNA
- Length
- 266 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hjc; 5'-D(*DC*DG*DG*DA*DT*DA*DT*DC*DC*DGP)-3'
- UniProt
- O28314
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hjc | protein | 120 | 31% helix, 33% strand | O28314 |
| B | Hjc | protein | 126 | 33% helix, 29% strand | O28314 |
| C, D | 5'-D(*DC*DG*DG*DA*DT*DA*DT*DC*DC*DGP)-3' | dna | 10 | — | — |
Ligands and binding sites
- HEZ · Hexane-1,6-diol · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.56 | 0.81 | 24 | HEZ |
| 2 | 158 | 0.55 | 0.82 | 25 | HEZ |
| 3 | 293 | 0.52 | 0.75 | 32 | empty |
| 4 | 115 | 0.45 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 909 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 462 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- B–C · 235 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 159 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 2WIW · Crystal structures of Holliday junction resolvases from Archaeoglobus fulgidus bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- O28314 · AlphaFold monomer V2.0 prediction for holliday junction resolvase hjc (O28314) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O28314
- Elsewhere: RCSB PDB 2WIW · PDBe 2WIW · UniProt O28314
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