MolNFT v1 · #184323 · protein + RNA
Thosea asigna virus rdrp domain in complex with RNA
7OM6 · RNA-dependent RNA polymerase: “Thosea asigna virus rdrp domain in complex with RNA”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #184323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OM6
- Type
- protein + RNA
- Length
- 1,292 residues
- Chains
- 6
- 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*U)-3')
- UniProt
- Q6A562
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 630 | 46% helix, 14% strand | Q6A562 |
| B | RNA-dependent RNA polymerase | protein | 634 | 46% helix, 14% strand | Q6A562 |
| C, D | RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3') | rna | 6 | — | — |
| E, F | RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3') | rna | 8 | — | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.81 | 0.83 | 66 | PEG |
| 2 | 1127 | 0.81 | 0.82 | 76 | PEG |
| 3 | 165 | 0.76 | 0.93 | 39 | empty |
| 4 | 214 | 0.72 | 0.88 | 42 | empty |
| 5 | 242 | 0.65 | 0.83 | 33 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2979 Ų buried · 53 hydrogen bonds · protein-protein
- B–E · 999 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–F · 929 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 713 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 710 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 7OM6 · Thosea asigna virus RdRP domain in complex with RNA · 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 Q6A562
- Elsewhere: RCSB PDB 7OM6 · PDBe 7OM6 · UniProt Q6A562
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