1KGK | pdb_00001kgk

Direct Observation of a Cytosine Analog that Forms Five Hydrogen Bonds to Guanosine; Guanyl G-Clamp

• PDB DOI: https://doi.org/10.2210/pdb1KGK/pdb
• NAKB: 1KGK

• Classification: DNA
• Mutation(s): No 


• Deposited: 2001-11-27 Released: 2001-12-21 
• Deposition Author(s): Wilds, C.J., Maier, M.A., Tereshko, V., Manoharan, M., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.124 (DCC) 
• R-Value Work: 
  0.121 (DCC) 

Literature

Direct Observation of a Cytosine Analogue that Forms Five Hydrogen Bonds to Guanosine: Guanidino G-Clamp

Wilds, C.J., Maier, M.A., Tereshko, V., Manoharan, M., Egli, M.

(2002) Angew Chem Int Ed Engl 41: 115-117

• PubMed: 12491456 
• DOI: https://doi.org/10.1002/1521-3773(20020104)41:1<115::aid-anie115>3.0.co;2-r
• Primary Citation Related Structures: 
  1KGK

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Organizational Affiliation: 
• Department of Biological Sciences, Vanderbilt University Nashville, TN 37235, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.83 kDa 
• Atom Count: 613 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*(GCK)P*GP*TP*AP*TP*AP*CP*GP*C)-3'	A, B	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPK	D [auth A]	SPERMINE (FULLY PROTONATED FORM) C10 H30 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-R
MOE	C [auth A], E [auth B]	METHOXY-ETHOXYL C3 H7 O2 ASQUQUOEFDHYGP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.124 (DCC) 
• R-Value Work:  0.121 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.52	α = 90
b = 43.02	β = 90
c = 46.68	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-21 
Deposition Author(s): Wilds, C.J., Maier, M.A., Tereshko, V., Manoharan, M., Egli, M.

Revision History  

• Version 1.0: 2001-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations