Research workbench
Structure of ruvb from thermus thermophilus HB8
Analyse Structure of ruvb from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HQC
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ruvb
- EC
- 3.6.1.3
- UniProt
- Q5SL87
- Ligands
- ADE, MG
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ruvb (EC 3.6.1.3) | protein | 314 | 44% helix, 11% strand | Q5SL87 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.58 | 0.80 | 25 | ADE |
| 2 | 102 | 0.54 | 0.83 | 17 | ADE |
| 3 | 150 | 0.44 | 0.76 | 22 | empty |
| 4 | 127 | 0.42 | 0.76 | 21 | empty |
| 5 | 85 | 0.39 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 676 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1HQC · Structure of ruvb from thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SL87 · AlphaFold monomer V2.0 prediction for holliday junction ATP-dependent DNA helicase ruvb… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q5SL87
- Elsewhere: RCSB PDB 1HQC · PDBe 1HQC · UniProt Q5SL87
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