Download MendeleyLoop-Deleted DNA Polymerase Theta Polymerase Domain in Complex with a dsDNA Overhang and an Allosteric Inhibitor
Fried, W., Chen, X.S.To be published.
9D6O | pdb_00009d6o
Loop-Deleted DNA Polymerase Theta Polymerase Domain in Complex with a dsDNA Overhang and an Allosteric Inhibitor
- PDB DOI: https://doi.org/10.2210/pdb9D6O/pdb
- 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
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.31 Å
- R-Value Free: 0.234 (Depositor), 0.242 (DCC)
- R-Value Work: 0.209 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.209 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase theta | 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 AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA Template | B [auth E] | 24 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA Primer | C [auth F] | 14 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1A2D (Subject of Investigation/LOI) Query on A1A2D | F [auth A] | 2-[3-(2-hydroxyethyl)-2-oxoimidazolidin-1-yl]-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate C21 H18 F7 N3 O4 SMVCNKJTRUVRLZ-UHFFFAOYSA-N |  | ||
| DG3 Query on DG3 | E [auth A] | 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O12 P3 HDRRAMINWIWTNU-NTSWFWBYSA-N |  | ||
| MG Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.31 Å
- R-Value Free: 0.234 (Depositor), 0.242 (DCC)
- R-Value Work: 0.209 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.209 (Depositor)
Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 172.356 | α = 90 |
| b = 172.356 | β = 90 |
| c = 62.415 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHASER | phasing |
| Coot | model building |
| DIALS | data reduction |
| DIALS | data scaling |
| BOS | data collection |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-08-20 Deposition Author(s): Fried, W., Chen, X.S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01 GM130889 |
Revision History (Full details and data files)
- Version 1.0: 2025-08-20
Type: Initial release
