Research workbench
Structure of viral RNA polymerase complex 1
Analyse Structure of viral RNA polymerase complex 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AVT
- Type
- protein + RNA
- Length
- 1,207 residues
- Chains
- 2
- 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
- GH3, CA
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor ts, elongation factor tu, linker, Q beta replicase | protein | 1203 | 37% helix, 22% strand | P0A6P3, P0A6N3, Q8LTE0 |
| T | RNA (5'-R(*AP*UP*CP*GP*CP*CP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · 2 copies · chains A, T
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.76 | 0.78 | 109 | empty |
| 2 | 937 | 0.74 | 0.78 | 61 | GH3, CA |
| 3 | 99 | 0.55 | 0.84 | 24 | empty |
| 4 | 136 | 0.54 | 0.82 | 25 | empty |
| 5 | 143 | 0.54 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–T · 666 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3AVT · Structure of viral RNA polymerase complex 1 · 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 0.18
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 3AVT · PDBe 3AVT · UniProt P0A6P3 · UniProt P0A6N3 · UniProt Q8LTE0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.