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Crystal structure of murine norovirus RNA dependent RNA polymerase in complex with 2THIOURIDINE(2TU)
Analyse Crystal structure of murine norovirus RNA dependent RNA polymerase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SFG
- Type
- protein
- Length
- 1,442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase
- UniProt
- Q80J95
- Ligands
- 2TU, MG, SO4
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase | protein | 480 | 37% helix, 16% strand | Q80J95 |
| B | RNA polymerase | protein | 474 | 39% helix, 17% strand | Q80J95 |
| C | RNA polymerase | protein | 488 | 41% helix, 16% strand | Q80J95 |
Ligands and binding sites
- 2TU · 1-(beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 28 copies · chains A, B, C
- GOL · Glycerol · additive · 25 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.70 | 0.75 | 113 | 2TU, GOL, MG |
| 2 | 1143 | 0.70 | 0.75 | 108 | 2TU, SO4 |
| 3 | 1043 | 0.70 | 0.74 | 93 | 2TU, SO4, GOL |
| 4 | 648 | 0.70 | 0.78 | 76 | GOL, SO4 |
| 5 | 263 | 0.54 | 0.76 | 33 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1275 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 438 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3SFG · crystal structure 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 3SFG · PDBe 3SFG · UniProt Q80J95
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