MolNFT v1 · #54485 · protein + DNA
Deinococcus radiodurans ISDRA2 transposase complexed with left end recognition and cleavage site and zn
2XQC: “Deinococcus radiodurans ISDRA2 transposase complexed with left end recognition and cleavage site and zn”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.58). MolNFT v1 #54485 on GenesisL1: 3D structure, binding…
- 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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