Research workbench
Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023
Analyse Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UPF
- 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
- Q80J95
- Ligands
- 0BU, SO4
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 476 | 40% helix, 17% strand | Q80J95 |
| B | RNA-dependent RNA polymerase | protein | 483 | 42% helix, 16% strand | Q80J95 |
| C | RNA-dependent RNA polymerase | protein | 471 | 42% helix, 17% strand | Q80J95 |
Ligands and binding sites
- 0BU · 8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid · ligand · 3 copies · chains A, 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.71 | 0.75 | 103 | 0BU, SO4 |
| 2 | 1191 | 0.71 | 0.75 | 109 | 0BU, SO4 |
| 3 | 805 | 0.68 | 0.75 | 75 | 0BU, SO4 |
| 4 | 547 | 0.66 | 0.77 | 50 | empty |
| 5 | 366 | 0.63 | 0.79 | 56 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1256 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3UPF · Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023 · 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 3UPF · PDBe 3UPF · UniProt Q80J95
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