Research workbench
Cryo-EM structure of HzTransib/TIR DNA transposon end complex (TEC)
Analyse Cryo-EM structure of HzTransib/TIR DNA transposon end complex (TEC) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PQY
- Type
- protein + DNA
- Length
- 984 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Helicoverpa zea; SYNTHETIC CONSTRUCT
- Molecule
- Putative DNA-mediated transposase; DNA (5'-D(P*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP*A…
- UniProt
- B0F0C5
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 4.2 · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative DNA-mediated transposase | protein | 460 | 45% helix, 12% strand | B0F0C5 |
| B, E | DNA (5'-D(P*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP*AP*A)-3') | dna | 16 | — | — |
| C, F | DNA (5'-D(P*TP*TP*TP*TP*CP*GP*AP*TP*CP*CP*AP*CP*CP*GP*TP*G)-3') | dna | 16 | — | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.86 | 0.90 | 105 | empty |
| 2 | 454 | 0.83 | 0.91 | 81 | empty |
| 3 | 180 | 0.79 | 0.94 | 42 | empty |
| 4 | 174 | 0.78 | 0.93 | 42 | empty |
| 5 | 80 | 0.69 | 0.94 | 20 | empty |
Interfaces
11 interfaces between chains.
- A–D · 1042 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 691 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- E–F · 690 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–F · 556 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 546 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6PQY · Cryo-EM structure of HZTRANSIB/TIR DNA transposon end complex (tec) · the same entry in another collection · chain A against A, 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 B0F0C5
- Elsewhere: RCSB PDB 6PQY · PDBe 6PQY · UniProt B0F0C5
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