Research workbench
Structure of variola topoisomerase non-covalently bound to DNA
Analyse Structure of variola topoisomerase non-covalently bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H7G
- Type
- protein + DNA
- Length
- 337 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3'; 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP…
- EC
- 5.99.1.2
- UniProt
- P32989
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3' | dna | 11 | — | — |
| Z | 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3' | dna | 14 | — | — |
| X | DNA topoisomerase 1 (EC 5.99.1.2) | protein | 312 | 51% helix, 15% strand | P32989 |
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 | 550 | 0.70 | 0.79 | 48 | empty |
| 2 | 149 | 0.53 | 0.80 | 18 | empty |
| 3 | 105 | 0.49 | 0.81 | 17 | empty |
| 4 | 86 | 0.49 | 0.82 | 28 | empty |
| 5 | 76 | 0.39 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- Z–X · 862 Ų buried · 20 hydrogen bonds · protein-nucleic
- Y–X · 773 Ų buried · 12 hydrogen bonds · protein-nucleic
- Y–Z · 468 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 2H7G · Structure of variola topoisomerase non-covalently bound to DNA · the same entry in another collection · chain Y against Y, 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 P32989
- Elsewhere: RCSB PDB 2H7G · PDBe 2H7G · UniProt P32989
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