Research workbench
Foot and mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA
Analyse Foot and mouth disease virus RNA-dependent RNA polymerase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WNE
- Type
- protein + RNA
- Length
- 489 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*AP*UP*GP*GP*GP*CP*C)-3'; 5'-R(*GP*GP*CP*CP*C)-3'; RNA-dependent RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q9QCE4
- Ligands
- MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*CP*AP*UP*GP*GP*GP*CP*C)-3' | rna | 8 | — | — |
| C | 5'-R(*GP*GP*CP*CP*C)-3' | rna | 5 | — | — |
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 476 | 39% helix, 16% strand | Q9QCE4 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.80 | 0.82 | 84 | MG |
| 2 | 156 | 0.60 | 0.84 | 24 | empty |
| 3 | 51 | 0.51 | 0.88 | 14 | empty |
| 4 | 65 | 0.49 | 0.85 | 16 | empty |
| 5 | 97 | 0.34 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1061 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–A · 622 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 264 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Compared structures
- 1WNE · Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with a… · the same entry in another collection · chain B against B, 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 Q9QCE4
- Elsewhere: RCSB PDB 1WNE · PDBe 1WNE · UniProt Q9QCE4
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