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

(-) 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 :  16 Jul 10  (Deposition) - 25 Aug 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Quadruplex, Oxtyricha Nova, Bsu-6039, Bsu6039, Anti-Parallel, Bimolecular, Macromolecule, Dna, G-Quadruplex, Telomere, Acridine, Fluorination (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 TELOMERE 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
2SNS1Ligand/Ion3,6-BIS(3-(3'-(S)-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 , HOH A:54 , HOH A:156 , HOH A:162 , DG B:1 , DT B:8 , DG B:9 , DG B:10 , DG B:12 , HOH B:21BINDING SITE FOR RESIDUE SNS 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:20 , HOH B:144BINDING SITE FOR RESIDUE K B 13

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NZ7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NZ7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NZ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NZ7)

(-) Exons   (0, 0)

(no "Exon" information available for 3NZ7)

(-) Sequences/Alignments

Asymmetric/Biological 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
                                           
                  3nz7 A  1 GGGGTTTTGGGG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  3nz7 B  1 GGGGTTTTGGGG 12
                                    10
   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 3NZ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NZ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NZ7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3NZ7)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 ]
    SNS  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nz7)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3nz7
    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 3NZ7)

(-) 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-FLUORINATED 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
3nyp 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