3C1P

Crystal Structure of an alternating D-Alanyl, L-Homoalanyl PNA

• PDB DOI: https://doi.org/10.2210/pdb3C1P/pdb
• NAKB: 3C1P

• Classification: PEPTIDE NUCLEIC ACID
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2008-01-23 Released: 2009-01-27 
• Deposition Author(s): Cuesta-Seijo, J.A., Sheldrick, G.M., Zhang, J., Diederichsen, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 

Literature

Continuous beta-turn fold of an alternating alanyl/homoalanyl peptide nucleic acid.

Cuesta-Seijo, J.A., Zhang, J., Diederichsen, U., Sheldrick, G.M.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1067-1070

• PubMed: 22868773 
• DOI: https://doi.org/10.1107/S090744491202118X
• Primary Citation of Related Structures:  
  3C1P


• PubMed Abstract: 
  

  The crystal structure of the PNA (peptide nucleic acid) oligomer H-Lys-HalG-AlaG-HalC-AlaG-HalC-AlaC-Lys-NH(2) (PNA1, amino acids with D-configuration are underlined, Ala = alanyl, Hal = homoalanyl) has been determined by ab initio direct methods and refined against 1.0 Å data. The asymmetric unit consists of a tetrameric cage with almost ideal Watson-Crick C-G base pairing of all the guanine and cytosine side-chain substituents. Each PNA strand has a 90° β-turn every second residue, stabilized by three hydrogen bonds between the backbone amides. The first, second, fifth and sixth bases stack on one side of the monomer and pair with the corresponding complementary bases of a second monomer to form a dimer. The two remaining bases on each side of the resulting dimer form Watson-Crick pairs with the complementary bases of a second dimer, leading to a unique cage structure. The extra methylene groups in the homoalanyl residues enable stacking of the bases with an optimal distance between base-planes but also with an appreciable lateral displacement (slide).

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Organizational Affiliation: 

Lehrstuhl für Strukturchemie, Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, Göttingen, 37077, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.07 kDa 
• Atom Count: 551 
• Modelled Residue Count: 32 
• Deposited Residue Count: 32 

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS	A, B, C, D	8	synthetic construct

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000110	A, B, C, D	DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.308	α = 90
b = 30.733	β = 99.53
c = 33.55	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXD	phasing
SHELXL-97	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Cuesta-Seijo, J.A., Sheldrick, G.M., Zhang, J., Diederichsen, U.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-25
  Changes: Database references
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2013-06-26
  Changes: Database references
• Version 1.5: 2014-11-26
  Changes: Structure summary
• Version 2.0: 2019-03-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations