Research workbench
Crystal structure of the ISHP608 transposase in complex with right end 31-mer DNA
Analyse Crystal structure of the ISHP608 transposase in complex with right end 31-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VHG
- Type
- protein + DNA
- Length
- 300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase orfa; Right end 31-mer
- UniProt
- Q933Z0
- Ligands
- MN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposase orfa | protein | 126 | 38% helix, 29% strand | Q933Z0 |
| B | Transposase orfa | protein | 127 | 39% helix, 28% strand | Q933Z0 |
| C | Right end 31-mer | dna | 23 | — | — |
| D | Right end 31-mer | dna | 24 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.62 | 0.77 | 52 | empty |
| 2 | 224 | 0.52 | 0.77 | 32 | empty |
| 3 | 170 | 0.49 | 0.78 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1710 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 601 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 372 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 371 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 2VHG · Crystal Structure of the ISHp608 Transposase in Complex with Right End 31-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 2VHG · PDBe 2VHG · UniProt Q933Z0
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