MolNFT v1 · #15117 · protein + DNA
Crystal structure of TN5 transposase complexed with resolved outside end DNA
1MUS · DNA transferred strand: “Crystal structure of TN5 transposase complexed with resolved outside end DNA”. X-ray diffraction, 2 ligands (MN, MG), 5 pockets (best druggability 0.67). MolNFT v1 #15117 on GenesisL1: 3D structure, binding…
- PDB
- 1MUS
- Type
- protein + DNA
- Length
- 498 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA transferred strand; DNA non-transferred strand; TN5 transposase
- UniProt
- Q46731
- Ligands
- MN, MG
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA transferred strand | dna | 20 | — | — |
| C | DNA non-transferred strand | dna | 20 | — | — |
| A | TN5 transposase | protein | 458 | 46% helix, 21% strand | Q46731 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains B, C, A
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.67 | 0.76 | 72 | EDO |
| 2 | 193 | 0.58 | 0.81 | 27 | empty |
| 3 | 245 | 0.57 | 0.79 | 29 | EDO |
| 4 | 145 | 0.42 | 0.75 | 23 | empty |
| 5 | 118 | 0.40 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 958 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- C–A · 885 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–A · 706 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 1MUS · crystal structure of Tn5 transposase complexed with resolved outside end 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 1MUS · PDBe 1MUS · UniProt Q46731
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