Research workbench
Structures of lassa and tacaribe viral nucleoproteins with or without 5 triphosphate dsrna substrate reveal a unique 3 -5 exoribonuclease mechanism to suppress type I interferon production
Analyse Structures of lassa and tacaribe viral nucleoproteins with or without 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GV3
- Type
- protein + RNA
- Length
- 215 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(GTP)P*GP*GP*C)-3'); RNA (5'-R(P*CP*GP*CP*CP*C)-3'); Nucleoprotein
- UniProt
- P13699
- Ligands
- MN, ZN
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (5'-R(*(GTP)P*GP*GP*C)-3') | rna | 4 | — | — |
| C | RNA (5'-R(P*CP*GP*CP*CP*C)-3') | rna | 4 | — | — |
| A | Nucleoprotein | protein | 207 | 38% helix, 19% strand | P13699 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.44 | 0.78 | 17 | empty |
| 2 | 105 | 0.43 | 0.78 | 16 | empty |
| 3 | 85 | 0.43 | 0.80 | 15 | empty |
| 4 | 69 | 0.31 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–A · 451 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–A · 239 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 191 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4GV3 · Structures of Lassa and Tacaribe viral nucleoproteins with or without 5 triphosphate… · the same entry in another collection · chain B against B, 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 P13699
- Elsewhere: RCSB PDB 4GV3 · PDBe 4GV3 · UniProt P13699
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