MolNFT v1 · #165523 · protein
In situ structure of bmcpv RNA dependent RNA polymerase at quiescent state
6TY8 · RNA-dependent RNA polymerase: “In situ structure of bmcpv RNA dependent RNA polymerase at quiescent state”. Electron microscopy, 1 ligand (GTA), 20 pockets (best druggability 0.86). MolNFT v1 #165523 on GenesisL1: 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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