Research workbench
In situ structure of bmcpv RNA dependent RNA polymerase at quiescent state
Analyse In situ structure of bmcpv RNA dependent RNA polymerase at quiescent state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TY8
- Type
- protein
- Length
- 1,694 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; Viral structural protein 4
- UniProt
- Q993A4, Q9IR43
- Ligands
- GTA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 1196 | 46% helix, 13% strand | Q993A4 |
| B | Viral structural protein 4 | protein | 498 | 41% helix, 13% strand | Q9IR43 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.86 | 0.88 | 109 | empty |
| 2 | 890 | 0.84 | 0.86 | 71 | empty |
| 3 | 145 | 0.81 | 0.98 | 31 | empty |
| 4 | 173 | 0.80 | 0.96 | 31 | empty |
| 5 | 59 | 0.73 | 0.99 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3303 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6TY8 · In situ structure of BmCPV RNA dependent RNA polymerase at quiescent state · 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 Q993A4
- Every structure of UniProt Q9IR43
- Elsewhere: RCSB PDB 6TY8 · PDBe 6TY8 · UniProt Q993A4 · UniProt Q9IR43
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