MolNFT v1 · #51858 · protein + DNA
Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site
2VJV · Transposase orfa: “Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA…”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.61). MolNFT v1 #51858 on GenesisL1: 3D…
- PDB
- 2VJV
- Type
- protein + DNA
- Length
- 314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase orfa; 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT…
- UniProt
- Q933Z0
- Ligands
- MG
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transposase orfa | protein | 125 | 42% helix, 28% strand | Q933Z0 |
| C, D | 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3' | dna | 26 | — | — |
| E, F | 5'-D(*DT*DA*DT*DT*DA*DCP)-3' | dna | 6 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.61 | 0.79 | 30 | MG |
| 2 | 282 | 0.61 | 0.80 | 28 | empty |
| 3 | 392 | 0.59 | 0.76 | 34 | empty |
| 4 | 53 | 0.33 | 0.78 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1269 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1001 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 927 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 578 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 563 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2VJV · Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin… · 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 Q933Z0
- Elsewhere: RCSB PDB 2VJV · PDBe 2VJV · UniProt Q933Z0
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