Research workbench
Dengue virus RNA dependent RNA polymerase with residues from the NS5 linker region
Analyse Dengue virus RNA dependent RNA polymerase with residues from the NS5 linker… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C11
- Type
- protein
- Length
- 1,196 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dengue virus type 3 RNA dependent RNA polymerase
- UniProt
- Q6DLV0
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dengue virus type 3 RNA dependent RNA polymerase | protein | 593 | 49% helix, 10% strand | Q6DLV0 |
| B | Dengue virus type 3 RNA dependent RNA polymerase | protein | 603 | 49% helix, 10% strand | Q6DLV0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.75 | 0.80 | 84 | empty |
| 2 | 503 | 0.66 | 0.78 | 69 | empty |
| 3 | 353 | 0.64 | 0.79 | 61 | empty |
| 4 | 452 | 0.62 | 0.76 | 34 | empty |
| 5 | 98 | 0.59 | 0.87 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1659 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4C11 · Dengue virus RNA dependent RNA polymerase with residues from the NS5 linker region · 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 Q6DLV0
- Elsewhere: RCSB PDB 4C11 · PDBe 4C11 · UniProt Q6DLV0
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