Research workbench
Ruva from mycobacterium tuberculosis
Analyse Ruva from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H5X
- Type
- protein
- Length
- 730 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holliday junction ATP-dependent DNA helicase ruva
- EC
- 3.6.1.-
- UniProt
- P66744
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.1.-) | protein | 183 | 48% helix, 22% strand | P66744 |
| B | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.1.-) | protein | 183 | 47% helix, 22% strand | P66744 |
| C | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.1.-) | protein | 182 | 48% helix, 23% strand | P66744 |
| D | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.1.-) | protein | 182 | 46% helix, 23% strand | P66744 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.83 | 0.96 | 32 | empty |
| 2 | 58 | 0.65 | 0.94 | 19 | empty |
| 3 | 441 | 0.62 | 0.76 | 51 | empty |
| 4 | 354 | 0.59 | 0.76 | 44 | empty |
| 5 | 357 | 0.58 | 0.76 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1199 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1192 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1186 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1167 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2H5X · RuvA from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
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 P66744
- Elsewhere: RCSB PDB 2H5X · PDBe 2H5X · UniProt P66744
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