Research workbench
Murine norovirus rdrp in complex with ppnds
Analyse Murine norovirus rdrp in complex with ppnds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O4R
- Type
- protein
- Length
- 1,430 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent-RNA-polymerase
- UniProt
- S4V9Y7
- Ligands
- 20V, SO4
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent-RNA-polymerase | protein | 476 | 42% helix, 17% strand | S4V9Y7 |
| B | RNA-dependent-RNA-polymerase | protein | 480 | 41% helix, 17% strand | S4V9Y7 |
| C | RNA-dependent-RNA-polymerase | protein | 474 | 43% helix, 18% strand | S4V9Y7 |
Ligands and binding sites
- 20V · 3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid · ligand · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 10 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.71 | 0.75 | 107 | 20V, SO4 |
| 2 | 1077 | 0.71 | 0.75 | 94 | 20V |
| 3 | 1122 | 0.70 | 0.75 | 105 | 20V |
| 4 | 625 | 0.70 | 0.78 | 80 | empty |
| 5 | 326 | 0.61 | 0.78 | 54 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1187 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4O4R · Murine Norovirus RdRp in complex with PPNDS · 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 S4V9Y7
- Elsewhere: RCSB PDB 4O4R · PDBe 4O4R · UniProt S4V9Y7
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