Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 :  STRUCTURE OF THE FIRST PARALLEL DNA QUADRUPLEX-DRUG COMPLEX
 
Authors :  G. R. Clark, P. D. Pytel, C. J. Squire, S. Neidle
Date :  22 Feb 03  (Deposition) - 15 Apr 03  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.17
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  G-4 Quadruplex Drug Complex, Parallel Quadruplex, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. R. Clark, P. D. Pytel, C. J. Squire, S. Neidle
Structure Of The First Parallel Dna Quadruplex-Drug Complex
J. Am. Chem. Soc. V. 125 4066 2003
PubMed-ID: 12670225  |  Reference-DOI: 10.1021/JA0297988
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*TP*GP*GP*GP*GP*T)-3'
    ChainsA, B, C, D
    EngineeredYES
    Other DetailsTGGGGT SYNTHESIZED BY OSWEL
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1DM13Ligand/IonDAUNOMYCIN
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1DM16Ligand/IonDAUNOMYCIN
2NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDT A:1001 , DG B:1008 , HOH B:1107 , HOH B:1124 , HOH B:1185 , DM1 C:27 , DG C:1014 , DG C:1015 , DG C:1016 , DM1 D:26BINDING SITE FOR RESIDUE DM1 B 25
2AC2SOFTWAREDG A:1002 , DG A:1003 , HOH A:1116 , DM1 B:25 , DM1 C:27 , DT C:1013 , DT C:1018 , DT D:1019 , DG D:1020 , HOH D:1101 , HOH D:1140BINDING SITE FOR RESIDUE DM1 D 26
3AC3SOFTWAREDT A:1001 , DM1 B:25 , DT C:1013 , DG C:1014 , DT C:1018 , HOH C:1106 , HOH C:1110 , HOH C:1126 , HOH C:1128 , HOH C:1129 , HOH C:1132 , HOH C:1134 , HOH C:1156 , HOH C:1159 , HOH C:1200 , DM1 D:26 , DT D:1019BINDING SITE FOR RESIDUE DM1 C 27
4AC4SOFTWAREDG A:1004 , DG A:1005 , DG B:1010 , DG B:1011 , NA C:29 , DG C:1016 , DG C:1017 , DG D:1022 , DG D:1023BINDING SITE FOR RESIDUE NA A 28
5AC5SOFTWARENA A:28 , NA A:30 , DG A:1003 , DG A:1004 , DG B:1009 , DG B:1010 , DG C:1015 , DG C:1016 , DG D:1021 , DG D:1022BINDING SITE FOR RESIDUE NA C 29
6AC6SOFTWAREDG A:1002 , DG A:1003 , DG B:1008 , DG B:1009 , NA C:29 , DG C:1014 , DG C:1015 , DG D:1020 , DG D:1021BINDING SITE FOR RESIDUE NA A 30

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O0K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O0K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O0K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O0K)

(-) Exons   (0, 0)

(no "Exon" information available for 1O0K)

(-) 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:6
                                       
                1o0k A 1001 TGGGGT 1006

Chain B from PDB  Type:DNA  Length:6
                                       
                1o0k B 1007 TGGGGT 1012

Chain C from PDB  Type:DNA  Length:6
                                       
                1o0k C 1013 TGGGGT 1018

Chain D from PDB  Type:DNA  Length:6
                                       
                1o0k D 1019 TGGGGT 1024

   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 1O0K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1O0K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O0K)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1O0K)

 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
    DM1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1o0k)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1o0k
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP | HSSP
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB 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 ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1O0K)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1O0K)