MolNFT v1 · #54423 · protein + DNA
Deinococcus radiodurans ISDRA2 transposase Y132F mutant complexed with left end recognition and cleavage site
2XO6: “Deinococcus radiodurans ISDRA2 transposase Y132F mutant complexed with left end recognition and cleavage site”. X-ray diffraction, 2 ligands (CD, MG), 5 pockets (best druggability 0.59). MolNFT v1 #54423 on GenesisL1: 3D structure…
- PDB
- 2XO6
- Type
- protein + DNA
- Length
- 328 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*G)-3'
- UniProt
- O83028
- Ligands
- CD, MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposase | protein | 134 | 40% helix, 30% strand | O83028 |
| B, E | DRA2 transposase left end recognition sequence | dna | 27 | — | — |
| C, F | 5'-D(*TP*TP*GP*AP*TP*G)-3' | dna | 6 | — | — |
| D | Transposase | protein | 128 | 42% helix, 31% strand | O83028 |
Ligands and binding sites
- CD · Cadmium ion · metal · 9 copies · chains A, C, D, B, F, E
- MG · Magnesium ion · metal · 8 copies · chains A, B, D, E
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.59 | 0.81 | 25 | empty |
| 2 | 200 | 0.58 | 0.81 | 21 | CD |
| 3 | 69 | 0.44 | 0.81 | 17 | empty |
| 4 | 62 | 0.39 | 0.80 | 18 | empty |
| 5 | 51 | 0.24 | 0.73 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–D · 2017 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 897 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 895 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 507 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–F · 501 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2XO6 · Deinococcus radiodurans ISDRA2 transposase Y132F mutant complexed with left end… · 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 2XO6 · PDBe 2XO6 · UniProt O83028
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