Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF GLYCOSYLASE DOMAIN OF MBD4 BOUND TO 5HMU CONTAINING DNA
 
Authors :  S. Morera, A. Vigouroux
Date :  21 Mar 12  (Deposition) - 08 Aug 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Hhh Dna Glycosylase Family, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Morera, I. Grin, A. Vigouroux, S. Couve, V. Henriot, M. Saparbaev, A. A. Ishchenko
Biochemical And Structural Characterization Of The Glycosylase Domain Of Mbd4 Bound To Thymine And 5-Hydroxymethyuracil-Containing Dna.
Nucleic Acids Res. V. 40 9917 2012
PubMed-ID: 22848106  |  Reference-DOI: 10.1093/NAR/GKS714

(-) Compounds

Molecule 1 - METHYL-CPG-BINDING DOMAIN PROTEIN 4
    ChainsA
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentGLYCOSYLASE DOMAIN OF MBD4 (RESIDUES 426-580)
    GeneMBD4, MED1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMETHYL-CPG-BINDING ENDONUCLEASE 1, METHYL-CPG-BINDING PROTEIN MBD4, MISMATCH-SPECIFIC DNA N-GLYCOSYLASE
 
Molecule 2 - DNA (5'-D(*CP*CP*AP*GP*CP*GP*(5HU)P*GP*CP*AP*GP*C)-3')
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
    ChainsD
    EngineeredYES
    Organism ScientificSYNTHETIC
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15HU1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4E9H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E9H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E9H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E9H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E9H)

(-) Exons   (0, 0)

(no "Exon" information available for 4E9H)

(-) Sequences/Alignments

Asymmetric/Biological 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:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e9h A 438 WTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEAHKLNKYHDWLWENH 574
                                   447       457       467       477       487       497       507       517       527       537       547       557       567       

Chain C from PDB  Type:DNA  Length:12
                                            
                 4e9h C   1 CCAGCGxGCAGC  12
                                  | 10  
                                  7-5HU 

Chain D from PDB  Type:DNA  Length:12
                                            
                 4e9h D   1 GCTGCGCGCTGG  12
                                    10  

   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 4E9H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E9H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E9H)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    5HU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4e9h)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4e9h)
 

(-) 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
  4e9h
    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 (structure derived) | HSSP (homology derived)
    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
  MBD4_HUMAN | O95243
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.-
    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
  MBD4_HUMAN | O95243
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MBD4_HUMAN | O952432moe 3iho 4dk9 4e9e 4e9f 4e9g 4ea4 4ea5 4lg7 4ofa 4ofe 4ofh 5chz

(-) Related Entries Specified in the PDB File

4e9e 4e9f 4e9g 4ea4 4eab