Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF EXOCYCLIC R,R N6,N6-(2,3-DIHYDROXY-1,4-BUTADIYL)-2'-DEOXYADENOSINE ADDUCT INDUCED BY 1,2,3,4-DIEPOXYBUTANE IN DNA
 
Authors :  E. A. Kowal, U. Seneviratne, S. Wickramaratne, K. E. Doherty, X. Cao, N. Tretyakova, M. P. Stone
Date :  05 Dec 13  (Deposition) - 28 May 14  (Release) - 04 Jun 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (8x)
NMR Structure *:  A,B  (1x)
Keywords :  B-Form Dna, 11-Mer, Deb Induced Adduct, Dhb-Da Adduct, N-Ras Codon 61 Sequence, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Kowal, U. Seneviratne, S. Wickramaratne, K. E. Doherty, X. Cao, N. Tretyakova, M. P. Stone
Structures Of Exocyclic R, R- And S, S-N(6), N(6)-(2, 3-Dihydroxybutan-1, 4-Diyl)-2'- Deoxyadenosine Adducts Induced By 1, 2, 3, 4-Diepoxybutane.
Chem. Res. Toxicol. V. 27 805 2014
PubMed-ID: 24741991  |  Reference-DOI: 10.1021/TX400472P

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
NMR Structure (8x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1RBD1Mod. Nucleotide(R,R)-N6,N6-(2,3-DIHYDROXY-1,4-BUTADIYL)-2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1RBD1Mod. Nucleotide(R,R)-N6,N6-(2,3-DIHYDROXY-1,4-BUTADIYL)-2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 2MHX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2MHX)

(-) Sequences/Alignments

NMR Structure
   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:11
                                          
                  2mhx A  1 CGGACaAGAAG 11
                                 |  10 
                                 6-RBD 


Chain B from PDB  Type:DNA  Length:11
                                          
                  2mhx B 12 CTTCTTGTCCG 22
                                    21
   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 2MHX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 2MHX)

 Visualization

(-) Interactive Views

NMR Structure
  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
    RBD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2mhx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mhx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2mhx
    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 2MHX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2MHX)