MolNFT v1 · #10646 · protein
Ruva-ruvb complex
1IXR · Holliday junction DNA helicase ruva: “Ruva-ruvb complex”. X-ray diffraction, 1 ligand (ANP), 3 pockets (best druggability 0.75). MolNFT v1 #10646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IXR
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holliday junction DNA helicase ruva; Ruvb
- EC
- 3.6.1.3
- UniProt
- Q9F1Q3, Q5SL87
- Ligands
- ANP
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holliday junction DNA helicase ruva | protein | 135 | 38% helix, 22% strand | Q9F1Q3 |
| B | Holliday junction DNA helicase ruva | protein | 191 | 47% helix, 16% strand | Q9F1Q3 |
| C | Ruvb (EC 3.6.1.3) | protein | 308 | 34% helix, 12% strand | Q5SL87 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.75 | 0.79 | 85 | ANP |
| 2 | 348 | 0.59 | 0.76 | 41 | empty |
| 3 | 61 | 0.30 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 701 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 575 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1IXR · RuvA-RuvB complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9F1Q3 · AlphaFold monomer V2.0 prediction for holliday junction ATP-dependent DNA helicase ruva… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q5SL87 · AlphaFold monomer V2.0 prediction for holliday junction ATP-dependent DNA helicase ruvb… · a predicted model of the same protein · chain C against A, TM-score 0.91
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 Q9F1Q3
- Every structure of UniProt Q5SL87
- Elsewhere: RCSB PDB 1IXR · PDBe 1IXR · UniProt Q9F1Q3 · UniProt Q5SL87
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