Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) 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')
    Chains: A
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synonym: TELOMERE REPEAT SEQUENCE
    Synthetic: YES

 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)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CCO)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA  Length:12
                                             
                3cco A 1001 TAGGGTTAGGGT 1012
                                  1010
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 3CCO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3CCO)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NII  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3cco)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3cco
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP | HSSP
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3CCO)

(-) Related Entries Specified in the PDB File

3cdm HUMAN TELOMERIC SEQUENCE BOUND TO SAME LIGAND