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(-) Description

Title :  A BIMOLECULAR ANTI-PARALLEL-STRANDED OXYTRICHA NOVA TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6-DISUBSTITUTED ACRIDINE BSU-6038
 
Authors :  N. H. Campbell, G. Parkinson, S. Neidle
Date :  23 Sep 08  (Deposition) - 14 Oct 08  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Quadruplex, Oxytricha Nova, Bsu-6038, Bsu6038, Anti- Parallel, Bimolecular, Macromolecule, G-Quadruplex, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. H. Campbell, M. Patel, A. B. Tofa, R. Ghosh, G. N. Parkinson, S. Neidle
Selectivity In Ligand Recognition Of G-Quadruplex Loops.
Biochemistry V. 48 1675 2009
PubMed-ID: 19173611  |  Reference-DOI: 10.1021/BI802233V
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
    Chains: A, B
    Engineered: YES
    Other Details: BIMOLECULAR ANTI-PARALLEL-STRANDED DNA QUADRUPLEX
    Other Details - Source: THE SEQUENCE OCCURS NATURALLY IN 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
2NCE1Ligand/Ion3,6-BIS[(3-MORPHOLINOPROPIONAMIDO)] ACRIDINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:1 , DG A:2 , DG A:11 , DG A:12 , K A:27 , DG B:15 , DG B:16 , DG B:21 , DG B:22 , K B:25BINDING SITE FOR RESIDUE K A 26
2AC2SOFTWAREDG A:2 , DG A:3 , DG A:10 , DG A:11 , K A:26 , K A:28 , DG B:14 , DG B:15 , DG B:22 , DG B:23BINDING SITE FOR RESIDUE K A 27
3AC3SOFTWAREDG A:3 , DG A:4 , DG A:9 , DG A:10 , K A:27 , DG B:13 , DG B:14 , DG B:23 , DG B:24BINDING SITE FOR RESIDUE K A 28
4AC4SOFTWAREDT A:6 , DT A:7 , DT A:8 , DG A:9 , DG B:13 , DT B:20 , DG B:21 , DG B:24 , HOH B:30BINDING SITE FOR RESIDUE NCE A 29
5AC5SOFTWAREDG A:1 , DG A:12 , K A:26 , DG B:16 , DT B:17 , DT B:19 , DG B:21 , HOH B:40 , HOH B:41BINDING SITE FOR RESIDUE K B 25

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EM2)

(-) Exons   (0, 0)

(no "Exon" information available for 3EM2)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:12
                                           
                  3em2 A  1 GGGGTTTTGGGG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  3em2 B 13 GGGGTTTTGGGG 24
                                    22
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3EM2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EM2)

(-) Pfam Domains  (0, 0)

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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 WITH A DIFFERENT LIGAND BSU -6039
3ce5 A BIMOLECULAR PARALLEL-STRANDED HUMAN TELOMERIC QUADRUPLEX IN COMPLEX WITH A 3,6,9-TRISUBSTITUTED ACRIDINE MOLECULE BRACO19
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