Research workbench
Cryo-EM structure of piggybac transposase strand transfer complex (stc)
Analyse Cryo-EM structure of piggybac transposase strand transfer complex (stc) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X67
- Type
- protein + DNA
- Length
- 1,116 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase; DNA (37-mer); DNA (47-mer); DNA (tdna)
- UniProt
- Q283G1
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Transposase | protein | 478 | 37% helix, 13% strand | Q283G1 |
| E | DNA (37-mer) | dna | 37 | — | — |
| F | DNA (47-mer) | dna | 47 | — | — |
| G, L | DNA (tdna) | dna | 8 | — | — |
| J | DNA (37-mer) | dna | 25 | — | — |
| K | DNA (47-mer) | dna | 35 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, D
- CA · Calcium ion · metal · 4 copies · chains C, G, K, E, D, F, L, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.88 | 0.89 | 114 | empty |
| 2 | 500 | 0.69 | 0.79 | 44 | empty |
| 3 | 257 | 0.68 | 0.84 | 43 | empty |
| 4 | 511 | 0.67 | 0.78 | 47 | empty |
| 5 | 156 | 0.60 | 0.84 | 21 | empty |
Interfaces
19 interfaces between chains.
- C–F · 1964 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–F · 1690 Ų buried · 114 hydrogen bonds · nucleic-nucleic
- D–K · 1596 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–E · 1327 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–F · 1172 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6X67 · Cryo-EM structure of piggyBac transposase strand transfer complex (STC) · the same entry in another collection · chain C against C, 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 Q283G1
- Elsewhere: RCSB PDB 6X67 · PDBe 6X67 · UniProt Q283G1
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