Research workbench
T. thermophilus ruvc in complex with holliday junction substrate
Analyse T. thermophilus ruvc in complex with holliday junction substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S16
- Type
- protein + DNA
- Length
- 380 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crossover junction endodeoxyribonuclease ruvc; DNA (33-mer); DNA…
- EC
- 3.1.22.4
- UniProt
- Q5SJC4
- Ligands
- NA, CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crossover junction endodeoxyribonuclease ruvc (EC 3.1.22.4) | protein | 158 | 47% helix, 22% strand | Q5SJC4 |
| B | Crossover junction endodeoxyribonuclease ruvc (EC 3.1.22.4) | protein | 165 | 47% helix, 20% strand | Q5SJC4 |
| C | DNA (33-mer) | dna | 33 | — | — |
| D | DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3') | dna | 12 | — | — |
| F | DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.69 | 0.76 | 69 | CL |
| 2 | 495 | 0.64 | 0.77 | 40 | empty |
| 3 | 208 | 0.49 | 0.76 | 36 | empty |
| 4 | 137 | 0.48 | 0.78 | 13 | empty |
| 5 | 60 | 0.43 | 0.82 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1265 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 684 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 580 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 401 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- C–F · 398 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Compared structures
- 6S16 · T. thermophilus RuvC in complex with Holliday junction substrate · the same entry in another collection · chain B against B, TM-score 1.00
- Q5SJC4 · AlphaFold monomer V2.0 prediction for crossover junction endodeoxyribonuclease ruvc… · 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 Q5SJC4
- Elsewhere: RCSB PDB 6S16 · PDBe 6S16 · UniProt Q5SJC4
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