Research workbench
Deinococcus radiodurans ISDRA2 transposase complexed with left end recognition and cleavage site and zn
Analyse Deinococcus radiodurans ISDRA2 transposase complexed with left end recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XQC
- Type
- protein + DNA
- Length
- 327 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase; DRA2 transposase left end recognition sequence; 5'-D(TP*TP*GP*AP*TP*GP)-3'
- UniProt
- O83028
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposase | protein | 129 | 43% helix, 31% strand | O83028 |
| B, E | DRA2 transposase left end recognition sequence | dna | 27 | — | — |
| C, F | 5'-D(TP*TP*GP*AP*TP*GP)-3' | dna | 6 | — | — |
| D | Transposase | protein | 132 | 43% helix, 30% strand | O83028 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, C, D, B, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.58 | 0.81 | 24 | empty |
| 2 | 192 | 0.58 | 0.81 | 23 | ZN |
| 3 | 118 | 0.48 | 0.79 | 18 | empty |
| 4 | 75 | 0.45 | 0.81 | 16 | empty |
| 5 | 68 | 0.41 | 0.80 | 13 | empty |
Interfaces
11 interfaces between chains.
- A–D · 1644 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 896 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–E · 889 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–F · 506 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 493 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 2XQC · Deinococcus radiodurans ISDRA2 transposase complexed with left end recognition and… · 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 O83028
- Elsewhere: RCSB PDB 2XQC · PDBe 2XQC · UniProt O83028
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