GL1X · GenesisL1 explorer

Research workbench

Structure of variola topoisomerase covalently bound to DNA

Analyse Structure of variola topoisomerase 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
2H7F
Type
protein + DNA
Length
339 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*T)-3'; 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)…
EC
5.99.1.2
UniProt
P32989
Pockets
4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
Y5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'dna11——
Z5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'dna14——
XDNA topoisomerase 1 (EC 5.99.1.2)protein31452% helix, 14% strandP32989

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13480.640.8039empty
23790.580.7538empty
31080.540.8426empty
4850.340.7415empty

Interfaces

3 interfaces between chains.

  • Z–X · 838 Ų buried · 17 hydrogen bonds · protein-nucleic
  • Y–X · 698 Ų buried · 12 hydrogen bonds · protein-nucleic
  • Y–Z · 472 Ų buried · 41 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

  • 2H7F · Structure of variola topoisomerase covalently bound to DNA · the same entry in another collection · chain Y against Y, TM-score 1.00

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.