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Crystal structure of thosea asigna virus RNA-dependent RNA polymerase (rdrp) complexed with cdp
Analyse Crystal structure of thosea asigna virus RNA-dependent RNA polymerase (rdrp)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CX6
- Type
- protein
- Length
- 1,328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- Q6A562
- Ligands
- CDP, MG, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 663 | 44% helix, 13% strand | Q6A562 |
| B | RNA-dependent RNA polymerase | protein | 665 | 44% helix, 13% strand | Q6A562 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- GOL · Glycerol · additive · 19 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.75 | 0.78 | 110 | SO4, GOL, CDP |
| 2 | 433 | 0.68 | 0.80 | 57 | SO4 |
| 3 | 328 | 0.65 | 0.81 | 45 | SO4, GOL, CDP |
| 4 | 129 | 0.51 | 0.81 | 20 | empty |
| 5 | 137 | 0.47 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3151 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 5CX6 · Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed… · 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 Q6A562
- Elsewhere: RCSB PDB 5CX6 · PDBe 5CX6 · UniProt Q6A562
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