Research workbench
Complex structure of viral RNA polymerase I
Analyse Complex structure of viral RNA polymerase I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VNU
- Type
- protein + RNA
- Length
- 1,215 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
- ATP, CA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor ts, elongation factor tu, linker, Q beta replicase | protein | 1203 | 35% helix, 20% strand | P0A6P3, P0A6N3, Q8LTE0 |
| G | RNA (5'-R(*CP*CP*CP*UP*AP*CP*CP*C)-3') | rna | 6 | — | — |
| T | RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3') | rna | 6 | — | — |
Ligands and binding sites
- ATP · Adenosine-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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.79 | 0.81 | 117 | ATP, CA |
| 2 | 1168 | 0.76 | 0.78 | 151 | empty |
| 3 | 543 | 0.66 | 0.78 | 52 | empty |
| 4 | 188 | 0.61 | 0.82 | 29 | empty |
| 5 | 148 | 0.51 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–G · 638 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–T · 537 Ų buried · 8 hydrogen bonds · protein-nucleic
- G–T · 318 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Compared structures
- 3VNU · Complex structure of viral RNA polymerase I · 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 3VNU · PDBe 3VNU · UniProt P0A6P3 · UniProt P0A6N3 · UniProt Q8LTE0
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