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Thosea asigna virus rdrp domain elongation complex
Analyse Thosea asigna virus rdrp domain elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OMA
- Type
- protein + RNA
- Length
- 2,576 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3'); RNA…
- UniProt
- Q6A562
- Ligands
- POP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA-dependent RNA polymerase | protein | 628 | 46% helix, 13% strand | Q6A562 |
| A | RNA-dependent RNA polymerase | protein | 629 | 46% helix, 14% strand | Q6A562 |
| C | RNA-dependent RNA polymerase | protein | 629 | 46% helix, 14% strand | Q6A562 |
| D | RNA-dependent RNA polymerase | protein | 630 | 46% helix, 14% strand | Q6A562 |
| E, G, I, L | RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3') | rna | 7 | — | — |
| F, H, J, K | RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3') | rna | 8 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 3 copies · chains B, G, A, E, C, I
- MG · Magnesium ion · metal · 5 copies · chains B, G, A, E, D, L, C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.80 | 0.82 | 73 | MG |
| 2 | 1047 | 0.79 | 0.81 | 60 | POP |
| 3 | 993 | 0.79 | 0.81 | 53 | POP |
| 4 | 968 | 0.79 | 0.81 | 56 | POP, MG |
| 5 | 174 | 0.78 | 0.94 | 32 | empty |
Interfaces
22 interfaces between chains.
- C–D · 2839 Ų buried · 46 hydrogen bonds · protein-protein
- B–A · 2800 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 982 Ų buried · 9 hydrogen bonds · protein-protein
- D–K · 964 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–H · 961 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 7OMA · Thosea asigna virus RdRP domain elongation complex · the same entry in another collection · chain K against K, 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 Q6A562
- Elsewhere: RCSB PDB 7OMA · PDBe 7OMA · UniProt Q6A562
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