4UQG

A new bio-isosteric base pair based on reversible bonding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

"Post-it" type connected DNA created with a reversible covalent cross-link.

Tomas-Gamasa, M.Serdjukow, S.Su, M.Muller, M.Carell, T.

(2015) Angew Chem Int Ed Engl 54: 796-800

  • DOI: 10.1002/anie.201407854
  • Primary Citation of Related Structures:  
    4UQG

  • PubMed Abstract: 
  • We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. Moreover, even enzymatic incorporation of the cross-link is possible ...

    We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. Moreover, even enzymatic incorporation of the cross-link is possible. The new principle can be used to stabilize DNA duplexes and nanostructures that otherwise require high salt concentrations, which may hinder biological applications.


    Organizational Affiliation

    Department of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München (Germany) http://www.carellgroup.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASEA579Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K5
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3'B10synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3'C10synthetic construct
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseD 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
DsucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.442α = 90
b = 93.996β = 90
c = 105.416γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references, Other, Refinement description
  • Version 1.2: 2015-01-28
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Advisory, Data collection
  • Version 1.4: 2019-02-20
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary