MolNFT v1 · #115946 · protein
Crystal structure of thosea asigna virus RNA-dependent RNA polymerase (rdrp) complexed with ATP and ssrna
5CYR: “Crystal structure of thosea asigna virus RNA-dependent RNA polymerase (rdrp) complexed with ATP and ssrna”. X-ray diffraction, 4 ligands (ATP, MG, PO4), 13 pockets (best druggability 0.74). MolNFT v1 #115946 on GenesisL1: 3D…
- PDB
- 5CYR
- Type
- protein
- Length
- 1,326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- Q6A562
- Ligands
- ATP, MG, PO4, SO4
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA-dependent RNA polymerase | protein | 664 | 41% helix, 12% strand | Q6A562 |
| A | RNA-dependent RNA polymerase | protein | 662 | 40% helix, 14% strand | Q6A562 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
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 | 1007 | 0.74 | 0.77 | 89 | ATP, SO4, PO4 |
| 2 | 629 | 0.73 | 0.80 | 84 | SO4, PO4 |
| 3 | 284 | 0.62 | 0.80 | 34 | empty |
| 4 | 179 | 0.59 | 0.82 | 32 | empty |
| 5 | 160 | 0.45 | 0.76 | 30 | MG |
Interfaces
1 interface between chains.
- B–A · 3205 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5CYR · Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed… · the same entry in another collection · chain B against B, 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 5CYR · PDBe 5CYR · UniProt Q6A562
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.