Research workbench
Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-434
Analyse Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-434 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XD0
- Type
- protein
- Length
- 589 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.012
- Source
- Dengue virus 3
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- A1XTB9
- Ligands
- V0M, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.012 · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 589 | 51% helix, 10% strand | A1XTB9 |
Ligands and binding sites
- V0M · 2-[({2-[(2,6-dichlorophenyl)amino]phenyl}acetyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.73 | 0.77 | 78 | V0M |
| 2 | 107 | 0.51 | 0.82 | 25 | empty |
| 3 | 66 | 0.48 | 0.84 | 18 | empty |
| 4 | 114 | 0.43 | 0.77 | 18 | empty |
| 5 | 117 | 0.36 | 0.73 | 16 | empty |
Compared structures
- 6XD0 · Dengue serotype 3 RNA-dependent RNA polymerase bound to nitd-434 · 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 A1XTB9
- Elsewhere: RCSB PDB 6XD0 · PDBe 6XD0 · UniProt A1XTB9
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