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Crystal structure of the complex of TDP1 with duplex DNA

Analyse Crystal structure of the complex of TDP1 with duplex DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5NWA
Type
protein + DNA
Length
883 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Tyrosyl-DNA phosphodiesterase 1; DNA (5'-D(P*AP*AP*TP*GP*CP*GP*CP*AP*TP*TP*A)-3')
EC
3.1.4.-
UniProt
Q9NUW8
Pockets
9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-)protein44127% helix, 23% strandQ9NUW8
CDNA (5'-D(P*AP*AP*TP*GP*CP*GP*CP*AP*TP*TP*A)-3')dna10——
BTyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-)protein43227% helix, 25% strandQ9NUW8

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111800.770.79117empty
21930.510.7723empty
32200.500.7531empty
41220.390.7520empty
5700.380.7913empty

Interfaces

2 interfaces between chains.

  • A–C · 606 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–B · 602 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

  • 5NWA · Crystal structure of the complex of Tdp1 with duplex DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9NUW8 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 1 (Q9NUW8) · a predicted model of the same protein · chain A against A, TM-score 0.99

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