MolNFT v1 · #51810 · protein + DNA
Crystal structure of the IS608 transposase in complex with left end 26-mer DNA
2VIH · Transposase orfa: “Crystal structure of the IS608 transposase in complex with left end 26-mer DNA”. X-ray diffraction, 5 pockets (best druggability 0.60). MolNFT v1 #51810 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2VIH
- Type
- protein + DNA
- Length
- 331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase orfa; 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP…
- UniProt
- Q933Z0
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposase orfa | protein | 151 | 42% helix, 25% strand | Q933Z0 |
| B | Transposase orfa | protein | 129 | 41% helix, 27% strand | Q933Z0 |
| C | 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3' | dna | 25 | — | — |
| D | 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3' | dna | 26 | — | — |
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 | 256 | 0.60 | 0.80 | 26 | empty |
| 2 | 292 | 0.56 | 0.76 | 29 | empty |
| 3 | 239 | 0.55 | 0.78 | 23 | empty |
| 4 | 56 | 0.40 | 0.81 | 19 | empty |
| 5 | 66 | 0.32 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2115 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 978 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 925 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 654 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 595 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2VIH · CRYSTAL STRUCTURE OF THE IS608 TRANSPOSASE IN COMPLEX WITH Left END 26-MER DNA · 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 2VIH · PDBe 2VIH · UniProt Q933Z0
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