6N0O | pdb_00006n0o

Crystal structure of Tdp1 catalytic domain in complex with compound XZ523

• PDB DOI: https://doi.org/10.2210/pdb6N0O/pdb

• Classification: DNA BINDING PROTEIN, Hydrolase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-07 Released: 2019-11-13 
• 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: 1.94 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Tdp1 catalytic domain

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: 104.92 kDa 
• Atom Count: 7,894 
• 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
K8G	E [auth A], H [auth B]	4-nitrobenzene-1,2-dicarboxylic acid C8 H5 N O6 SLBQXWXKPNIVSQ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.767	α = 90
b = 105.153	β = 90
c = 194.212	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: 2019-11-13 
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: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description