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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE
 
Authors :  J. M. Vargason, B. F. Eichman, P. S. Ho
Date :  21 Jun 00  (Deposition) - 28 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  B-Dna, E-Dna, Double Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Vargason, B. F. Eichman, P. S. Ho
The Extended And Eccentric E-Dna Structure Induced By Cytosine Methylation Or Bromination.
Nat. Struct. Biol. V. 7 758 2000
PubMed-ID: 10966645  |  Reference-DOI: 10.1038/78985
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
    Chains: A, B, C, D, E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): A    
Biological Unit 2 (1x):  BC  
Biological Unit 3 (1x):    DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SPM2Ligand/IonSPERMINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SPM-1Ligand/IonSPERMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SPM1Ligand/IonSPERMINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SPM1Ligand/IonSPERMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:1 , DG A:2 , DC A:3 , DG A:4 , HOH A:34 , DG B:7 , DG B:8 , DG D:19 , DC E:29 , DC E:30BINDING SITE FOR RESIDUE SPM D 31
2AC2SOFTWAREDC A:3 , DG A:4 , DG B:7 , DG B:8 , DC B:9 , HOH B:44 , DG C:16BINDING SITE FOR RESIDUE SPM B 32

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F6C)

(-) Exons   (0, 0)

(no "Exon" information available for 1F6C)

(-) 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
                                     
                  1f6c A  1 GGCGCC  6


Chain B from PDB  Type:DNA  Length:6
                                     
                  1f6c B  7 GGCGCC 12


Chain C from PDB  Type:DNA  Length:6
                                     
                  1f6c C 13 GGCGCC 18


Chain D from PDB  Type:DNA  Length:6
                                     
                  1f6c D 19 GGCGCC 24


Chain E from PDB  Type:DNA  Length:6
                                     
                  1f6c E 25 GGCGCC 30
   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 1F6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1F6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F6C)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1F6C)

 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
    SPM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f6c)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  1f6c
    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 1F6C)

(-) Related Entries Specified in the PDB File

1f69 B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE
1f6e A-DNA HEXAMER GGCGM5CC
1f6i E-DNA HEXAMER GGCGM5CC
1f6j E-DNA HEXAMER GGCGBR5CC