Download MendeleyStructural Insights into a DNA Polymerase Reading the Xeno Nucleic Acid HNA
Gutfreund, C., Betz, K.(2024) Nucleic Acids Res
9EMI
KOD-H4 DNA polymerase mutant in a ternary complex containing six HNA nucleotides and a non-hydrolyzable triphosphate
- PDB DOI: https://doi.org/10.2210/pdb9EMI/pdb
- NAKB: 9EMI
- Classification: TRANSFERASE
- Organism(s): Thermococcus kodakarensis KOD1, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-03-08 Released: 2024-11-13
- Funding Organization(s): German Research Foundation (DFG)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.27 Å
- R-Value Free: 0.265
- R-Value Work: 0.234
- R-Value Observed: 0.236
Starting Model: experimental
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This is version 1.0 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 | 774 | Thermococcus kodakarensis KOD1 | Mutation(s): 0 EC: 2.7.7.7 |  | |
UniProt | |||||
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore D0VWU9 Go to UniProtKB: D0VWU9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0VWU9 | ||||
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*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*CP*A*(XG4))-3') | B [auth P] | 13 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*(6HA)P*(6HA)P*(6HC)P*(6HT)P*(6HG)P*(6HT)P*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | C [auth T] | 16 | 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 | F [auth A] | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine C10 H17 N6 O12 P3 DWGAAFQEGIMTIA-KVQBGUIXSA-N |  | ||
| EDO Query on EDO | D [auth A], G [auth P], I [auth T] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A], H [auth P] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.27 Å
- R-Value Free: 0.265
- R-Value Work: 0.234
- R-Value Observed: 0.236
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 111.454 | α = 90 |
| b = 151.548 | β = 90 |
| c = 70.406 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-11-13 Deposition Author(s): Gutfreund, C., Betz, K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| German Research Foundation (DFG) | Germany | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-11-13
Type: Initial release
