Research workbench
The RNA-dependent RNA polymerase domain of dengue 3 NS5
Analyse The RNA-dependent RNA polymerase domain of dengue 3 NS5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J00
- Type
- protein
- Length
- 575 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.14
- Source
- Dengue virus 3
- Molecule
- Genome polyprotein
- UniProt
- Q5I3C1
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.14 · 1 distinct chain · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 575 | 47% helix, 10% strand | Q5I3C1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.65 | 0.75 | 66 | empty |
| 2 | 202 | 0.51 | 0.77 | 30 | empty |
| 3 | 70 | 0.45 | 0.82 | 20 | empty |
| 4 | 85 | 0.39 | 0.77 | 25 | empty |
Compared structures
- 6J00 · The RNA-dependent RNA polymerase domain of dengue 3 NS5 · 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 Q5I3C1
- Elsewhere: RCSB PDB 6J00 · PDBe 6J00 · UniProt Q5I3C1
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