Download MendeleyStructure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
Koag, M.-C., Lee, S.To be published.
6E3X
Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
- PDB DOI: https://doi.org/10.2210/pdb6E3X/pdb
- NAKB: 6E3X
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2018-07-15 Released: 2019-04-03
- Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.266
- R-Value Work: 0.192
- R-Value Observed: 0.196
This is version 1.2 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 beta | 335 | Homo sapiens | Mutation(s): 0 Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06746 (Homo sapiens) Explore P06746 Go to UniProtKB: P06746 | |||||
PHAROS: P06746 GTEx: ENSG00000070501 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P06746 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*CP*GP*AP*CP*(A38) P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | B [auth T] | 16 | Homo sapiens |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3') | C [auth P] | 10 | Homo sapiens |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*GP*TP*CP*GP*G)-3') | 5 | Homo sapiens |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DZ4 Query on DZ4 | I [auth A] | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine C10 H17 N6 O11 P3 WKIPJDSLGCBQCU-RRKCRQDMSA-N |  | ||
| MG Query on MG | G [auth A], H [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth A], F [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.266
- R-Value Work: 0.192
- R-Value Observed: 0.196
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.964 | α = 90 |
| b = 78.948 | β = 106.53 |
| c = 54.823 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
| PHASER | phasing |
| PHENIX | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-04-03 Deposition Author(s): Koag, M.-C., Lee, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) | United States | ES-26676 |
Revision History (Full details and data files)
- Version 1.0: 2019-04-03
Type: Initial release - Version 1.1: 2019-12-18
Changes: Author supporting evidence - Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
