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(-) Description

Title :  ONE SUGAR PUCKER FITS ALL: PAIRING VERSATILITY DESPITE CONFORMATIONAL UNIFORMITY IN TNA
 
Authors :  P. S. Pallan, C. J. Wilds, Z. Wawrzak, R. Krishnamurthy, A. Eschenmoser, M. Egli
Date :  01 Jul 03  (Deposition) - 13 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.16
Chains :  Asym./Biol. Unit :  A,B
Keywords :  A-Dna, Hydrogen Bonding, Nucleic Acid Etiology, Tetrose, Four Carbon Sugar, X-Ray Crystallography, Nucleic Acid Analogue (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. S. Pallan, C. J. Wilds, Z. Wawrzak, R. Krishnamurthy, A. Eschenmoser, M. Egli
Why Does Tna Cross-Pair More Strongly With Rna Than With Dna? An Answer From X-Ray Analysis.
Angew. Chem. Int. Ed. Engl. V. 42 5893 2003
PubMed-ID: 14673929  |  Reference-DOI: 10.1002/ANIE.200352553
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'
    ChainsA, B
    EngineeredYES
    Other DetailsA-DNA DECAMER DUPLEX WITH TNA-ADENINE AND 2'-METHOXY-THYMINE MODIFICATIONS
    Other Details - SourceCHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
12MU2Mod. Nucleotide2',5-DIMETHYLURIDINE-5'-MONOPHOSPHATE
2FA22Mod. Nucleotide5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL DIHYDROGEN PHOSPHATE
3SPM1Ligand/IonSPERMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:9 , HOH A:504 , HOH A:520 , HOH A:521 , HOH A:522 , DG B:113 , DT B:114 , DG B:119 , HOH B:534 , HOH B:573 , HOH B:577BINDING SITE FOR RESIDUE SPM B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PWF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PWF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1PWF)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:DNA/RNA  Length:10
                                          
                 1pwf A   1 GCGTAuaCGC  10
                                 || 10
                                 6-2MU
                                  7-FA2

Chain B from PDB  Type:DNA/RNA  Length:10
                                          
                 1pwf B 111 GCGTAuaCGC 120
                                 ||120
                               116-2MU
                                117-FA2

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1PWF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PWF)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

1n1o CRYSTAL STRUCTURE OF A B-FORM DNA DUPLEX CONTAINING (L)- ALPHA-THREOFURANOSYL (3'-->2') NUCLEOSIDES: A FOUR-CARBON SUGAR IS EASILY ACCOMMODATED INTO THE BACKBONE OF DNA