Download MendeleyStructures of human DNA polymerase beta inserting bases opposite templating O6MG
Koag, M.C., Min, K., Monzingo, A.F., Lee, S.To be published.
4MF8
Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template O6MG and incoming CTP
- PDB DOI: https://doi.org/10.2210/pdb4MF8/pdb
- NAKB: 4MF8
- Classification: TRANSFERASE/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-08-27 Released: 2014-08-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.32 Å
- R-Value Free: 0.272
- R-Value Work: 0.209
- R-Value Observed: 0.212
wwPDB Validation 3D Report Full Report
This is version 1.1 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 | 329 | 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 | |
| template | B [auth T] | 16 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| primer | C [auth P] | 11 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | H [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| MG Query on MG | E [auth A], I [auth P] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | F [auth A], G [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.32 Å
- R-Value Free: 0.272
- R-Value Work: 0.209
- R-Value Observed: 0.212
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.036 | α = 90 |
| b = 79.721 | β = 107.38 |
| c = 54.989 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| StructureStudio | data collection |
| DENZO | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2014-08-27 Deposition Author(s): Koag, M.C., Min, K., Monzingo, A.F., Lee, S.
Revision History (Full details and data files)
- Version 1.0: 2014-08-27
Type: Initial release - Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations
