9D6N | pdb_00009d6n

Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor

PDB DOI: https://doi.org/10.2210/pdb9D6N/pdb
NAKB: 9D6N

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

Deposited: 2024-08-15 Released: 2025-08-20
Deposition Author(s): Fried, W., Chen, X.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.237 (Depositor), 0.238 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor

Fried, W., Chen, X.S.

To be published.

Macromolecule Content

Total Structure Weight: 170.62 kDa
Atom Count: 12,006
Modeled Residue Count: 1,347
Deposited Residue Count: 1,380
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase theta	A, D [auth B]	652	Homo sapiens	Mutation(s): 0 Gene Names: POLQ, POLH EC: 3.6.4.12 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 2.7.7.49 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens) Explore O75417 Go to UniProtKB: O75417
PHAROS: O75417 GTEx: ENSG00000051341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75417
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA Template	B [auth E], E [auth C]	24	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA Primer	C [auth F], F [auth D]	14	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A2C (Subject of Investigation/LOI) Query on A1A2C Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	2-{3-[(2R)-3-(dimethylamino)-2-hydroxypropyl]-2-oxoimidazolidin-1-yl}-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate C₂₄ H₂₅ F₇ N₄ O₄ XOWJYFCVFGFEFB-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
DG3 Query on DG3 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ HDRRAMINWIWTNU-NTSWFWBYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]