Download MendeleyThe spontaneous base substitution mechanisms of human DNA polymerase beta
Koag, M.C., Lee, S.To be published.
4PHP
Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP and MANGANESE
- PDB DOI: https://doi.org/10.2210/pdb4PHP/pdb
- NAKB: 4PHP
- Classification: Transferase,Lyase/DNA
- Organism(s): synthetic construct, Homo sapiens
- Expression System: Enterobacteria phage L1
- Mutation(s): No
- Deposited: 2014-05-06 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: 2.60 ?
- R-Value Free: 0.262
- R-Value Work: 0.181
- R-Value Observed: 0.185
This is version 1.3 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), 4.2.99.18 (UniProt) |  |
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: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | A [auth T] | 16 | synthetic construct |  | |
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(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') | B [auth P] | 10 | 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 | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XG4 Query on XG4 | I [auth A] | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine C10 H17 N6 O12 P3 DWGAAFQEGIMTIA-KVQBGUIXSA-N |  | ||
| MN Query on MN | E [auth A], F [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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: 2.60 ?
- R-Value Free: 0.262
- R-Value Work: 0.181
- R-Value Observed: 0.185
- Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 50.701 | ¦Á = 90 |
| b = 79.327 | ¦Â = 107.58 |
| c = 55.474 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| 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: 2017-09-20
Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary - Version 1.2: 2019-12-18
Changes: Author supporting evidence - Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description
