6N0D | pdb_00006n0d

Crystal structure of Tdp1 catalytic domain in complex with compound XZ575

PDB DOI: https://doi.org/10.2210/pdb6N0D/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.193 (Depositor), 0.192 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Tdp1 catalytic domain in complex with compound XZ575

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.

Macromolecule Content

Total Structure Weight: 104.75 kDa
Atom Count: 8,058
Modeled Residue Count: 873
Deposited Residue Count: 922
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NUW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K8J Query on K8J Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	4-fluorobenzene-1,2-dicarboxylic acid C₈ H₅ F O₄ OMCXTFVBNCFZMY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.193 (Depositor), 0.192 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.058	α = 90
b = 105.429	β = 90
c = 193.915	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Burke Jr., T.R.

Revision History (Full details and data files)

Version 1.0: 2019-11-13
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.