Research workbench
Crystal structure of the thap domain from D. melanogaster P-element transposase in complex with its natural DNA binding site
Analyse Crystal structure of the thap domain from D. melanogaster P-element transposase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDE
- Type
- protein + DNA
- Length
- 94 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3'; 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3'…
- UniProt
- Q7M3K2
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3' | dna | 10 | — | — |
| B | 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3' | dna | 10 | — | — |
| C | Transposable element P transposase | protein | 74 | 23% helix, 16% strand | Q7M3K2 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 95 | 0.43 | 0.79 | 21 | empty |
| 2 | 111 | 0.43 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 637 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 576 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 441 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3KDE · Crystal structure of the THAP domain from D. melanogaster P-element transposase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7M3K2 · AlphaFold monomer V2.0 prediction for transposable element P transposase (Q7M3K2) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q7M3K2
- Elsewhere: RCSB PDB 3KDE · PDBe 3KDE · UniProt Q7M3K2
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