Research workbench
Crystal structure of TN5 transposase complexed with me DNA
Analyse Crystal structure of TN5 transposase complexed with me DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MM8
- Type
- protein + DNA
- Length
- 495 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Me DNA transferred strand; Me DNA non-transferred strand; TN5 transposase
- UniProt
- Q46731
- Ligands
- MN
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Me DNA transferred strand | dna | 20 | — | — |
| C | Me DNA non-transferred strand | dna | 20 | — | — |
| A | TN5 transposase | protein | 455 | 46% helix, 20% strand | Q46731 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.63 | 0.75 | 57 | empty |
| 2 | 276 | 0.59 | 0.78 | 35 | empty |
| 3 | 205 | 0.54 | 0.78 | 24 | empty |
| 4 | 110 | 0.48 | 0.80 | 21 | empty |
| 5 | 150 | 0.47 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 932 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- C–A · 851 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–A · 766 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 1MM8 · Crystal structure of Tn5 Transposase complexed with ME DNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q46731 · AlphaFold monomer V2.0 prediction for transposase for transposon TN5 (Q46731) · a predicted model of the same protein · chain A 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 Q46731
- Elsewhere: RCSB PDB 1MM8 · PDBe 1MM8 · UniProt Q46731
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