Research workbench
Crystal structure of the IS608 transposase in complex with the complete right end 35-mer DNA and manganese
Analyse Crystal structure of the IS608 transposase in complex with the complete right… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VJU
- Type
- protein + DNA
- Length
- 334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase orfa; Right end 35-mer
- UniProt
- Q933Z0
- Ligands
- MN
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposase orfa | protein | 129 | 42% helix, 28% strand | Q933Z0 |
| B | Transposase orfa | protein | 135 | 39% helix, 27% strand | Q933Z0 |
| C, D | Right end 35-mer | dna | 35 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.60 | 0.80 | 25 | empty |
| 2 | 369 | 0.59 | 0.77 | 36 | empty |
| 3 | 231 | 0.59 | 0.80 | 20 | empty |
| 4 | 121 | 0.44 | 0.77 | 22 | empty |
| 5 | 83 | 0.38 | 0.77 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2008 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1156 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–D · 1149 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–D · 619 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 587 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 2VJU · Crystal structure of the IS608 transposase in complex with the complete Right end 35-mer… · 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 2VJU · PDBe 2VJU · UniProt Q933Z0
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