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(-) Description

Title :  A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE LIGAND CONTAINING BIS-3-FLUOROPYRROLIDINE END SIDE CHAINS
 
Authors :  N. H. Campbell, S. Neidle
Date :  15 Jul 10  (Deposition) - 25 Aug 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Quadruplex, Oxtyricha Nova, Bsu-6039, Bsu6039, Anti-Parallel, Bimolecular, Macromolecule, Dna, G-Quadruplex, Telomere, Acridine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. H. Campbell, D. L. Smith, A. P. Reszka, S. Neidle, D. O'Hagan
Fluorine In Medicinal Chemistry: Beta-Fluorination Of Peripheral Pyrrolidines Attached To Acridine Ligands Affect Their Interactions With G-Quadruplex Dna.
Org. Biomol. Chem. V. 9 1328 2011
PubMed-ID: 21221451  |  Reference-DOI: 10.1039/C0OB00886A

(-) Compounds

Molecule 1 - 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
    Chains: A, B
    Engineered: YES
    Other Details: THIS TELOMERIC SEQUENCE OCCURS NATURALLY IN THE ORGANISM OXYTRICHA NOVA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1K4Ligand/IonPOTASSIUM ION
2RNR1Ligand/Ion3,6-BIS(3-(3'-(R)-FLUOROPYRROLINDINO)PROPIONAMIDO)ACRIDINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:1 , DG A:2 , DG A:11 , DG A:12 , K A:15 , DG B:3 , DG B:4 , DG B:9 , DG B:10 , K B:13BINDING SITE FOR RESIDUE K A 14
2AC2SOFTWAREDG A:2 , DG A:3 , DG A:10 , DG A:11 , K A:14 , K A:16 , DG B:2 , DG B:3 , DG B:10 , DG B:11BINDING SITE FOR RESIDUE K A 15
3AC3SOFTWAREDG A:3 , DG A:4 , DG A:9 , DG A:10 , K A:15 , DG B:1 , DG B:2 , DG B:11 , DG B:12BINDING SITE FOR RESIDUE K A 16
4AC4SOFTWAREDT A:6 , DT A:7 , DG A:9 , DG B:1 , DT B:8 , DG B:9 , DG B:12 , HOH B:26BINDING SITE FOR RESIDUE RNR A 17
5AC5SOFTWAREDG A:1 , DG A:12 , K A:14 , DG B:4 , DT B:5 , DT B:7 , DG B:9 , HOH B:14BINDING SITE FOR RESIDUE K B 13

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NYP)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:DNA  Length:12
                                           
                  3nyp A  1 GGGGTTTTGGGG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  3nyp B  1 GGGGTTTTGGGG 12
                                    10
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 Classification and Annotation

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(-) Gene Ontology  (0, 0)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1jpq SAME QUADRUPLEX STRUCTURE IN ITS NATIVE FORM (LIGAND-FREE)
1jrn SAME QUADRUPLEX STRUCTURE IN ITS NATIVE FORM (LIGAND-FREE)
1l1h SAME QUADRUPLEX STRUCTURE BOUND TO THE NON-FLOURINATED FORM OF THE LIGAND BSU-6039
3ce5 A BIMOLECULAR PARALLEL-STRANDED HUMAN TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6,9-TRISUBSTITUTED ACRIDINE MOLECULAR BRACO19
3em2 A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6038
3eqw A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6042 IN SMALL UNIT CELL
3eru A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6045
3es0 A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6048
3et8 A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6054
3eui A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6042 IN LARGE UNIT CELL
3eum A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6066
3nz7