3C1P

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

Summary for 3C1P

• Entry DOI: 10.2210/pdb3c1p/pdb
• Related PRD ID: PRD_000110
• Descriptor: Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS (2 entities in total)
• Functional Keywords: synthetic, peptide nucleic acid, pna, alanyl, homoalanyl, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 6074.01

Authors

Cuesta-Seijo, J.A.,Sheldrick, G.M.,Zhang, J.,Diederichsen, U. (deposition date: 2008-01-23, release date: 2009-01-27, Last modification date: 2024-11-06)

Primary citation

Cuesta-Seijo, J.A.,Zhang, J.,Diederichsen, U.,Sheldrick, G.M.
Continuous beta-turn fold of an alternating alanyl/homoalanyl peptide nucleic acid.
Acta Crystallogr.,Sect.D, 68:1067-1070, 2012

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).

PubMed: 22868773
DOI: 10.1107/S090744491202118X

Experimental method

X-RAY DIFFRACTION (1 Å)