MolNFT v1 · #122435 · protein + DNA
Tomato spotted wilt tospovirus nucleocapsid protein-ssdna complex
5IP3 · Nucleoprotein: “Tomato spotted wilt tospovirus nucleocapsid protein-ssdna complex”. X-ray diffraction, 8 pockets (best druggability 0.85). MolNFT v1 #122435 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IP3
- Type
- protein + DNA
- Length
- 749 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; DNA (5'-D(P*TP*TP*TP*TP*T)-3'); DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3'); DNA…
- UniProt
- F4ZD19
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nucleoprotein | protein | 246 | 54% helix, 2% strand | F4ZD19 |
| C | Nucleoprotein | protein | 246 | 57% helix, 3% strand | F4ZD19 |
| A | Nucleoprotein | protein | 241 | 59% helix, 2% strand | F4ZD19 |
| D | DNA (5'-D(P*TP*TP*TP*TP*T)-3') | dna | 4 | — | — |
| E | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3') | dna | 7 | — | — |
| F | DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') | dna | 5 | — | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.85 | 0.86 | 127 | empty |
| 2 | 272 | 0.66 | 0.83 | 36 | empty |
| 3 | 129 | 0.58 | 0.84 | 10 | empty |
| 4 | 129 | 0.49 | 0.79 | 14 | empty |
| 5 | 80 | 0.41 | 0.79 | 17 | empty |
Interfaces
10 interfaces between chains.
- C–A · 1980 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1850 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1762 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 1030 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–F · 902 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5IP3 · Tomato spotted wilt tospovirus nucleocapsid protein-ssDNA 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 5IP3 · PDBe 5IP3 · UniProt F4ZD19
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