Research workbench
Tomato spotted wilt tospovirus nucleocapsid protein-ssrna complex
Analyse Tomato spotted wilt tospovirus nucleocapsid protein-ssrna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IP2
- Type
- protein + RNA
- Length
- 702 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; RNA (5'- R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')…
- UniProt
- F4ZD19
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nucleoprotein | protein | 233 | 62% helix, 3% strand | F4ZD19 |
| C, A | Nucleoprotein | protein | 229 | 61% helix, 3% strand | F4ZD19 |
| E | RNA (5'- R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 5 | — | — |
| F, D | RNA (5'-D(P*UP*UP*U)-3') | rna | 3 | — | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.79 | 0.81 | 112 | empty |
| 2 | 108 | 0.61 | 0.87 | 24 | empty |
| 3 | 54 | 0.55 | 0.89 | 18 | empty |
| 4 | 80 | 0.52 | 0.85 | 22 | empty |
| 5 | 271 | 0.50 | 0.74 | 31 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1815 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 1702 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1624 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 668 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 516 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5IP2 · Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex · 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 F4ZD19
- Elsewhere: RCSB PDB 5IP2 · PDBe 5IP2 · UniProt F4ZD19
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