6MYZ | pdb_00006myz

Crystal structure of Tdp1 catalytic domain in complex with compound XZ520

• PDB DOI: https://doi.org/10.2210/pdb6MYZ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-02 Released: 2019-11-06 
• Deposition Author(s): Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.83 kDa 
• Atom Count: 7,918 
• Modeled Residue Count: 876 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 1	A, B	461	Homo sapiens	Mutation(s): 0  Gene Names: TDP1 EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUW8 (Homo sapiens) Explore Q9NUW8  Go to UniProtKB:  Q9NUW8
PHAROS:  Q9NUW8 GTEx:  ENSG00000042088

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K7D	C [auth A]	4-oxo-8-phenyl-1,4-dihydroquinoline-3-carboxylic acid C16 H11 N O3 IYZQCKZKSCOMCY-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.065	α = 90
b = 105.586	β = 90
c = 194.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S.

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description