MolNFT v1 · #81447 · protein
Crystal structures of murine norovirus RNA-dependent RNA polymerase in complex with suramin
3UR0: “Crystal structures of murine norovirus RNA-dependent RNA polymerase in complex with suramin”. X-ray diffraction, 2 ligands (SVR, SO4), 14 pockets (best druggability 0.71). MolNFT v1 #81447 on GenesisL1: 3D structure, binding sites…
- PDB
- 3UR0
- Type
- protein
- Length
- 1,425 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- Q80J95
- Ligands
- SVR, 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 | 475 | 43% helix, 17% strand | Q80J95 |
| B | RNA-dependent RNA polymerase | protein | 476 | 41% helix, 17% strand | Q80J95 |
| C | RNA-dependent RNA polymerase | protein | 474 | 42% helix, 17% strand | Q80J95 |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · 3 copies · chains B, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
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 | 747 | 0.71 | 0.77 | 80 | empty |
| 2 | 1035 | 0.71 | 0.75 | 86 | SVR, SO4 |
| 3 | 673 | 0.67 | 0.76 | 56 | SO4 |
| 4 | 496 | 0.63 | 0.76 | 52 | empty |
| 5 | 598 | 0.63 | 0.75 | 62 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1280 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UR0 · Crystal structures of murine norovirus RNA-dependent RNA polymerase in complex with… · 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 Q80J95
- Elsewhere: RCSB PDB 3UR0 · PDBe 3UR0 · UniProt Q80J95
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