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Crystal structure of human topoisomerase I DNA complex

Analyse Crystal structure of human topoisomerase I DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1EJ9
Type
protein + DNA
Length
527 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T )-3'); DNA…
EC
5.99.1.2
UniProt
P11387
Pockets
8 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
CDNA (5'- D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T )-3')dna22——
DDNA (5'- D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T )-3')dna22——
ADNA topoisomerase I (EC 5.99.1.2)protein48345% helix, 14% strandP11387

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110390.860.8798empty
23730.730.8552empty
32330.650.8425empty
4740.460.8214empty
5550.390.8116empty

Interfaces

3 interfaces between chains.

  • C–D · 949 Ų buried · 92 hydrogen bonds · nucleic-nucleic
  • C–A · 929 Ų buried · 24 hydrogen bonds · protein-nucleic
  • D–A · 888 Ų buried · 23 hydrogen bonds · protein-nucleic

Compared structures

  • 1EJ9 · Crystal structure of human topoisomerase I DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
  • P11387 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P11387) · a predicted model of the same protein · chain A against A, TM-score 0.99

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