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(-) Description

Title :  STRUCTURAL ADAPTATION AND CONSERVATION IN QUADRUPLEX-DRUG RECOGNITION
 
Authors :  G. N. Parkinson, S. Neidle
Date :  26 Feb 08  (Deposition) - 23 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Quadruplex, Dna, Propeller, Dimeric, Human Telomere Parallel Stranded, Ligand, Complex, Naphthalene Diimidine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. N. Parkinson, F. Cuenca, S. Neidle
Topology Conservation And Loop Flexibility In Quadruplex-Drug Recognition: Crystal Structures Of Inter- And Intramolecular Telomeric Dna Quadruplex-Drug Complexes
J. Mol. Biol. V. 381 1145 2008
PubMed-ID: 18619463  |  Reference-DOI: 10.1016/J.JMB.2008.06.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
    ChainsA
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS
    SynonymTELOMERE REPEAT SEQUENCE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1K3Ligand/IonPOTASSIUM ION
2NA1Ligand/IonSODIUM ION
3NII3Ligand/Ion2,7-BIS[3-(DIMETHYLAMINO)PROPYL]-4,9-BIS[(3-HYDROXYPROPYL)AMINO]BENZO[LMN][3,8]PHENANTHROLINE-1,3,6,8(2H,7H)-TETRONE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NA-1Ligand/IonSODIUM ION
3NII6Ligand/Ion2,7-BIS[3-(DIMETHYLAMINO)PROPYL]-4,9-BIS[(3-HYDROXYPROPYL)AMINO]BENZO[LMN][3,8]PHENANTHROLINE-1,3,6,8(2H,7H)-TETRONE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:1011 , HOH A:1013 , HOH A:1015 , HOH A:1020BINDING SITE FOR RESIDUE NA A 4
2AC2SOFTWAREK A:31 , DG A:1004 , DG A:1005 , DG A:1010 , DG A:1011BINDING SITE FOR RESIDUE K A 30
3AC3SOFTWAREK A:30 , K A:32 , DG A:1003 , DG A:1004 , DG A:1009 , DG A:1010BINDING SITE FOR RESIDUE K A 31
4AC4SOFTWAREK A:31 , DG A:1003 , DG A:1009BINDING SITE FOR RESIDUE K A 32
5AC5SOFTWAREDG A:1005 , DT A:1006 , DG A:1011BINDING SITE FOR RESIDUE NII A 1
6AC6SOFTWARENII A:3 , DT A:1007 , DG A:1009 , HOH A:1016BINDING SITE FOR RESIDUE NII A 2
7AC7SOFTWARENII A:2BINDING SITE FOR RESIDUE NII A 3

(-) SS Bonds  (0, 0)

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

(-) 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 Unit
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Chain A from PDB  Type:DNA  Length:12
                                             
                3cco A 1001 TAGGGTTAGGGT 1012
                                  1010  

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3cdm HUMAN TELOMERIC SEQUENCE BOUND TO SAME LIGAND