Research workbench
The structure of a TY3 retrotransposon icosahedral capsid
Analyse The structure of a TY3 retrotransposon icosahedral capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R24
- Type
- protein
- Length
- 1,419 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposon TY3-I gag-pol polyprotein
- EC
- 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- Q7LHG5
- Pockets
- 2 · best druggability 0.32
Structure
electron microscopy · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, I | Transposon TY3-I gag-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 159 | 69% helix, 0% strand | Q7LHG5 |
| B, F, H | Transposon TY3-I gag-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 155 | 71% helix, 0% strand | Q7LHG5 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.32 | 0.72 | 18 | empty |
| 2 | 63 | 0.24 | 0.71 | 18 | empty |
Interfaces
10 interfaces between chains.
- F–G · 115 Ų buried · 0 hydrogen bonds · protein-protein
- H–I · 107 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 91 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R24 · The structure of a Ty3 retrotransposon icosahedral capsid · the same entry in another collection · chain I against I, TM-score 1.00
- Q7LHG5 · AlphaFold monomer V2.0 prediction for transposon TY3-I gag-pol polyprotein (Q7LHG5) · a predicted model of the same protein · chain B against A, TM-score 0.47
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 Q7LHG5
- Elsewhere: RCSB PDB 6R24 · PDBe 6R24 · UniProt Q7LHG5
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