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 :  5-OME-DU CONTAINING DNA 8MER
 
Authors :  J. Sheng, A. E. A. Hassan, W. Zhang, J. Gan, Z. Huang
Date :  16 Feb 10  (Deposition) - 09 Mar 10  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dna, Oligonucleotide, 2'-Seme, 5-Ome, Selenium, 5-Methoxy-Uridine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sheng, W. Zhang, A. E. Hassan, J. Gan, A. S. Soares, S. Geng, Y. Ren, Z. Huang
Hydrogen Bond Formation Between The Naturally Modified Nucleobase And Phosphate Backbone.
Nucleic Acids Res. V. 40 8111 2012
PubMed-ID: 22641848  |  Reference-DOI: 10.1093/NAR/GKS426

(-) Compounds

Molecule 1 - 5'-D(*GP*(UMS)P*GP*(T5O)P*AP*CP*AP*C)-3'
    Chains: A
    Engineered: YES
    Other Details: SYNTHESIZED BY SOLID PHASE SYNTHESIZER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2T5O1Mod. Nucleotide2'-DEOXY-5-METHOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
3UMS1Mod. Nucleotide2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2T5O2Mod. Nucleotide2'-DEOXY-5-METHOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
3UMS2Mod. Nucleotide2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREUMS A:2 , DG A:3 , HOH A:120BINDING SITE FOR RESIDUE MG A 11

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LTR)

(-) 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:8
                                      
                   3ltr A 1 GxGxACAC 8
                             | |    
                             | |    
                             2-UMS  
                               4-T5O
   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 3LTR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    T5O  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ltr)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3ltr
    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 3LTR)

(-) Related Entries Specified in the PDB File

3ijk 3ltu