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

(-) Description

Title :  THE STRUCTURE OF THE DICKERSON SEQUENCE WITH AN INCORPORATED CENA RESIDUE
 
Authors :  K. Robeyns, L. Van Meervelt
Date :  22 Mar 07  (Deposition) - 05 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Cena, Sugar Modification, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Robeyns, P. Herdewijn, L. Van Meervelt
Influence Of The Incorporation Of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto The Sequence D(Cgcgaattcgcg).
Nucleic Acids Res. V. 36 1407 2008
PubMed-ID: 18160414  |  Reference-DOI: 10.1093/NAR/GKM1132
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR) P*DTP*DTP*DCP*DGP*DCP*DG)-3'
    Chains: A, B
    Engineered: YES
    Other Details: THE XAR (CYCLOHEXENE NUCLEIC ACID) RESIDUES AS WELL AS THE OLIGOMER SEQUENCE WERE SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NCO3Ligand/IonCOBALT HEXAMMINE(III)
2XAR2Mod. Nucleotide[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NCO-1Ligand/IonCOBALT HEXAMMINE(III)
2XAR2Mod. Nucleotide[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1NCO6Ligand/IonCOBALT HEXAMMINE(III)
2XAR2Mod. Nucleotide[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC A:3 , DG A:4 , DG A:12 , XAR B:6 , DT B:7 , DC B:9 , DG B:10 , HOH B:109 , HOH B:111 , HOH B:112BINDING SITE FOR RESIDUE NCO B 101
2AC2SOFTWAREDG A:2 , DC A:9 , DG A:10 , HOH A:16 , DT B:7 , HOH B:113 , HOH B:127BINDING SITE FOR RESIDUE NCO B 102
3AC3SOFTWAREDC B:3 , DG B:4 , DC B:11 , DG B:12BINDING SITE FOR RESIDUE NCO B 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P8D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P8D)

(-) Exons   (0, 0)

(no "Exon" information available for 2P8D)

(-) 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
                                           
                  2p8d A  1 CGCGAxTTCGCG 12
                                 |  10  
                                 6-XAR  


Chain B from PDB  Type:DNA  Length:11
                                          
                  2p8d B  2 GCGAxTTCGCG 12
                                |   11 
                                6-XAR
   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 2P8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P8D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2P8D)

 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
    NCO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    XAR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p8d)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  2p8d
    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 2P8D)

(-) Related Entries Specified in the PDB File

2h0n CONTAINS THE SAME SYNTHETIC NUCLEOSIDES