Research workbench
Murine norovirus RNA-dependent-RNA-polymerase in complex with compound 6, a suramin derivative
Analyse Murine norovirus RNA-dependent-RNA-polymerase in complex with compound 6, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NRU
- Type
- protein
- Length
- 2,866 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase
- UniProt
- S4V9Y7
- Ligands
- 2NG, MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase | protein | 477 | 41% helix, 16% strand | S4V9Y7 |
| B | RNA dependent RNA polymerase | protein | 482 | 43% helix, 16% strand | S4V9Y7 |
| C | RNA dependent RNA polymerase | protein | 478 | 41% helix, 16% strand | S4V9Y7 |
| D | RNA dependent RNA polymerase | protein | 479 | 43% helix, 17% strand | S4V9Y7 |
| E | RNA dependent RNA polymerase | protein | 477 | 42% helix, 16% strand | S4V9Y7 |
| F | RNA dependent RNA polymerase | protein | 473 | 42% helix, 17% strand | S4V9Y7 |
Ligands and binding sites
- 2NG · 4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic acid · ligand · 7 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.75 | 0.84 | 56 | empty |
| 2 | 953 | 0.70 | 0.75 | 94 | 2NG |
| 3 | 832 | 0.69 | 0.75 | 84 | empty |
| 4 | 274 | 0.68 | 0.83 | 41 | empty |
| 5 | 738 | 0.67 | 0.75 | 77 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1199 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1195 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1189 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 489 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 435 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4NRU · Murine Norovirus RNA-dependent-RNA-polymerase in complex with Compound 6, a suramin… · 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 4NRU · PDBe 4NRU · UniProt S4V9Y7
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