Research workbench
Crystal structure of the IS608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complex
Analyse Crystal structure of the IS608 transposase in complex with left end 29-mer DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FI8
- Type
- protein + DNA
- Length
- 648 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transposase; DNA 29-mer (LE29); DNA 6-mer (T6')
- UniProt
- Q933Z0
- Ligands
- CA
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative transposase | protein | 127 | 39% helix, 28% strand | Q933Z0 |
| B, G | Putative transposase | protein | 128 | 41% helix, 28% strand | Q933Z0 |
| C, D, I, J | DNA 29-mer (LE29) | dna | 29 | — | — |
| E, F, K, L | DNA 6-mer (T6') | dna | 6 | — | — |
| H | Putative transposase | protein | 125 | 42% helix, 30% strand | Q933Z0 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, E, C, D, F, G, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.61 | 0.76 | 42 | empty |
| 2 | 315 | 0.60 | 0.79 | 29 | CA |
| 3 | 336 | 0.60 | 0.78 | 30 | CA |
| 4 | 252 | 0.59 | 0.80 | 22 | empty |
| 5 | 288 | 0.58 | 0.78 | 29 | CA |
Interfaces
22 interfaces between chains.
- A–B · 2087 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 1941 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 945 Ų buried · 20 hydrogen bonds · protein-nucleic
- H–J · 940 Ų buried · 21 hydrogen bonds · protein-nucleic
- G–I · 927 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 6FI8 · Crystal structure of the IS608 transposase in complex with left end 29-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 6FI8 · PDBe 6FI8 · UniProt Q933Z0
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