Download MendeleyBypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta
Patra, A., Egli, M.To be published.
5F9N
CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dCMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION
- PDB DOI: https://doi.org/10.2210/pdb5F9N/pdb
- NAKB: 5F9N
- Classification: Transferase/DNA
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-12-09 Released: 2016-12-21
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.23 Å
- R-Value Free: 0.210
- R-Value Work: 0.158
- R-Value Observed: 0.160
Starting Model: experimental
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This is version 1.4 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase eta | 435 | Homo sapiens | Mutation(s): 0 Gene Names: POLH, RAD30, RAD30A, XPV EC: 2.7.7.7 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9Y253 (Homo sapiens) Explore Q9Y253 Go to UniProtKB: Q9Y253 | |||||
PHAROS: Q9Y253 GTEx: ENSG00000170734 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y253 | ||||
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*AP*TP*(GNE)P*AP*TP*GP*AP*CP*GP*CP*T)-3') | B [auth T] | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') | C [auth P] | 8 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 0KX Query on 0KX | D [auth A] | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine C9 H17 N4 O12 P3 STYMTWKSQLVXJN-SHYZEUOFSA-N |  | ||
| GOL Query on GOL | G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A], F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.23 Å
- R-Value Free: 0.210
- R-Value Work: 0.158
- R-Value Observed: 0.160
- Space Group: P 61
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.08 | α = 90 |
| b = 99.08 | β = 90 |
| c = 81.89 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-12-21
Type: Initial release - Version 1.1: 2017-09-27
Changes: Author supporting evidence - Version 1.2: 2019-01-16
Changes: Data collection, Source and taxonomy - Version 1.3: 2019-12-25
Changes: Author supporting evidence - Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
