9B3B | pdb_00009b3b

Structure of TDP1 complexed with compound IB09

PDB DOI: https://doi.org/10.2210/pdb9B3B/pdb

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

Deposited: 2024-03-18 Released: 2024-09-25
Deposition Author(s): Lountos, G.T., Zhao, X.Z., Barakat, I., Wang, W., Agama, K., Al Mahmud, M.R., Pommier, Y., Burke, T.R.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.189 (Depositor), 0.191 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of TDP1 complexed with compound IB09

Lountos, G.T., Zhao, X.Z., Barakat, I., Wang, W., Agama, K., Al Mahmud, M.R., Pommier, Y., Burke, T.R.

To be published.

Macromolecule Content

Total Structure Weight: 105.82 kDa
Atom Count: 8,133
Modeled Residue Count: 879
Deposited Residue Count: 922
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AIM (Subject of Investigation/LOI) Query on A1AIM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	(8M)-8-{4-(benzylcarbamoyl)-2-[(fluorosulfonyl)oxy]phenyl}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid C₂₄ H₁₇ F N₂ O₇ S OZKSCFDEHDSVKF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]