6MYZ

Crystal structure of Tdp1 catalytic domain in complex with compound XZ520


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.661 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of Tdp1 catalytic domain in complex with compound XZ520

Lountos, G.T.Zhao, X.Z.Kiselev, E.Tropea, J.E.Needle, D.Burke Jr., T.R.Pommier, Y.Waugh, D.S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 1
A, B
461Homo sapiensMutation(s): 0 
Gene Names: TDP1
EC: 3.1.4.-
Find proteins for Q9NUW8 (Homo sapiens)
Go to Gene View: TDP1
Go to UniProtKB:  Q9NUW8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K7D
Query on K7D

Download SDF File 
Download CCD File 
A
4-oxo-8-phenyl-1,4-dihydroquinoline-3-carboxylic acid
C16 H11 N O3
IYZQCKZKSCOMCY-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.661 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.065α = 90.00
b = 105.586β = 90.00
c = 194.670γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release