Research workbench
Crystal structure of tomato aspermy virus 2B in complex with siRNA
Analyse Crystal structure of tomato aspermy virus 2B in complex with siRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CZ3
- Type
- protein + RNA
- Length
- 298 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A)-3'); RNA (5'…
- UniProt
- Q8UYT3
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | RNA (5'- R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A)-3') | rna | 19 | — | — |
| F, H | RNA (5'- R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G)-3') | rna | 19 | — | — |
| A, B, D | Protein 2B | protein | 56 | 82% helix, 0% strand | Q8UYT3 |
| C | Protein 2B | protein | 54 | 80% helix, 0% strand | Q8UYT3 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.87 | 0.88 | 86 | empty |
| 2 | 797 | 0.86 | 0.89 | 61 | empty |
| 3 | 298 | 0.73 | 0.87 | 30 | empty |
| 4 | 83 | 0.37 | 0.76 | 12 | empty |
| 5 | 69 | 0.31 | 0.75 | 11 | empty |
Interfaces
24 interfaces between chains.
- E–F · 943 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- G–H · 936 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- H–C · 847 Ų buried · 30 hydrogen bonds · protein-nucleic
- F–A · 831 Ų buried · 27 hydrogen bonds · protein-nucleic
- G–D · 823 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- 3CZ3 · Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA · the same entry in another collection · chain E against E, 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 Q8UYT3
- Elsewhere: RCSB PDB 3CZ3 · PDBe 3CZ3 · UniProt Q8UYT3
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