Download MendeleyThe spontaneous base substitution mechanisms of human DNA polymerase beta
Koag, M.C., Lee, S.To be published.
4PH5
Structure of human DNA polymerase beta complexed with a nicked DNA containing a AC at N-1 position and GC at N position
- PDB DOI: https://doi.org/10.2210/pdb4PH5/pdb
- NAKB: 4PH5
- Classification: Transferase,Lyase/DNA
- Organism(s): synthetic construct, Homo sapiens
- Expression System: Enterobacteria phage L1
- Mutation(s): No
- Deposited: 2014-05-04 Released: 2015-05-06
- Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.261
- R-Value Work: 0.191
- R-Value Observed: 0.195
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase beta | D [auth A] | 326 | 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 | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | A [auth T] | 16 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') | B [auth P] | 11 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*GP*TP*CP*GP*G)-3') | C [auth D] | 5 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | I [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| MG Query on MG | E [auth A], F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | G [auth A], H [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.261
- R-Value Work: 0.191
- R-Value Observed: 0.195
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.613 | α = 90 |
| b = 80.377 | β = 107.61 |
| c = 55.294 | γ = 90 |
| Software Name | Purpose |
|---|---|
| StructureStudio | data collection |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| REFMAC | refinement |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-05-06 Deposition Author(s): Koag, M.C., Lee, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) | United States | ES23101 |
Revision History (Full details and data files)
- Version 1.0: 2015-05-06
Type: Initial release - Version 1.1: 2015-05-13
Changes: Structure summary - Version 1.2: 2017-09-20
Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary - Version 1.3: 2019-12-18
Changes: Author supporting evidence - Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description
