Research workbench
Complex structure of viral RNA polymerase II
Analyse Complex structure of viral RNA polymerase II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VNV
- Type
- protein + RNA
- Length
- 1,218 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor ts, elongation factor tu, linker, Q beta replicase; RNA…
- UniProt
- P0A6P3, P0A6N3, Q8LTE0
- Ligands
- CH1, CA
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor ts, elongation factor tu, linker, Q beta replicase | protein | 1203 | 38% helix, 24% strand | P0A6P3, P0A6N3, Q8LTE0 |
| G | RNA (5'-R(*CP*CP*CP*UP*AP*CP*C)-3') | rna | 7 | — | — |
| T | RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3') | rna | 8 | — | — |
Ligands and binding sites
- CH1 · 3'-deoxy-cytidine-5'-triphosphate · ligand · chains A, G, T
- CA · Calcium ion · metal · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.78 | 0.86 | 52 | CH1, CA |
| 2 | 337 | 0.73 | 0.86 | 46 | empty |
| 3 | 391 | 0.64 | 0.78 | 43 | empty |
| 4 | 118 | 0.62 | 0.87 | 32 | empty |
| 5 | 161 | 0.56 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–G · 732 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–T · 719 Ų buried · 13 hydrogen bonds · protein-nucleic
- G–T · 350 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 3VNV · Complex structure of viral RNA polymerase II · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6P3 · AlphaFold monomer V2.0 prediction for elongation factor ts (P0A6P3) · a predicted model of the same protein · chain A against A, TM-score 0.20
- P0A6N3 · AlphaFold monomer V2.0 prediction for elongation factor tu (P0A6N3) · a predicted model of the same protein · chain A against A, TM-score 0.19
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 P0A6P3
- Every structure of UniProt P0A6N3
- Every structure of UniProt Q8LTE0
- Elsewhere: RCSB PDB 3VNV · PDBe 3VNV · UniProt P0A6P3 · UniProt P0A6N3 · UniProt Q8LTE0
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