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

(-) Description

Title :  SOLUTION STRUCTURE AND DYNAMIC ANALYSIS OF CHICKEN MBD2 METHYL BINDING DOMAIN BOUND TO A TARGET METHYLATED DNA SEQUENCE
 
Authors :  D. C. Williams Jr. , J. N. Scarsdale Jr.
Date :  18 May 10  (Deposition) - 18 May 11  (Release) - 07 Sep 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
NMR Structure *:  A,B,C  (1x)
Keywords :  Dna Binding Domain, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Scarsdale, H. D. Webb, G. D. Ginder, D. C. Williams
Solution Structure And Dynamic Analysis Of Chicken Mbd2 Methyl Binding Domain Bound To A Target-Methylated Dna Sequence.
Nucleic Acids Res. V. 39 6741 2011
PubMed-ID: 21531701  |  Reference-DOI: 10.1093/NAR/GKR262

(-) Compounds

Molecule 1 - METHYL-CPG-BINDING DOMAIN PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET32A
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-71
    Gene: MBD2
    Organism Common: BANTAM,CHICKENS
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
 
Molecule 2 - DNA (5'-D(*GP*GP*AP*AP*TP*(5CM)P*GP*GP*CP*(TED)P*C)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*AP*GP*CP*(5CM)P*GP*AP*TP*(TED)P*CP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
NMR Structure (20x): ABC
NMR Structure * (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

NMR Structure (3, 6)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
3TED2Mod. Nucleotide5-[(1E)-14-CARBOXY-10,13-BIS(CARBOXYMETHYL)-3,8-DIOXO-4,7,10,13-TETRAAZATETRADEC-1-EN-1-YL]-2'-DEOXYURIDINE5'-(DIHYDROGEN PHOSPHATE)
NMR Structure * (2, 4)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3TED2Mod. Nucleotide5-[(1E)-14-CARBOXY-10,13-BIS(CARBOXYMETHYL)-3,8-DIOXO-4,7,10,13-TETRAAZATETRADEC-1-EN-1-YL]-2'-DEOXYURIDINE5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETED C:119BINDING SITE FOR RESIDUE MN C 301
2AC2SOFTWARETED B:109BINDING SITE FOR RESIDUE MN B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KY8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KY8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KY8)

(-) Exons   (0, 0)

(no "Exon" information available for 2KY8)

(-) 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:PROTEIN  Length:70
 aligned with Q5EFL0_CHICK | Q5EFL0 from UniProtKB/TrEMBL  Length:257

    Alignment length:70
                                    11        21        31        41        51        61        71
         Q5EFL0_CHICK     2 DKQGRTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVDLSCFDFRTGKMM  71
               SCOP domains d2ky8a_ A: automated matches                                           SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains MBD-2ky8A01 A:3-72                                                     Pfam domains
         Sec.struct. author ....eee........eeeeee.........eeeeee.....eeehhhhhhhhhh.......ee....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2ky8 A   3 DKQGRTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVDLSCFDFRTGKMM  72
                                    12        22        32        42        52        62        72


Chain B from PDB  Type:DNA  Length:11
                                           
                 2ky8 B 100 GGAATcGGCtC 110
                                 | 109 
                               105-5CM 
                                   109-TED


Chain C from PDB  Type:DNA  Length:11
                                           
                 2ky8 C 111 GAGCcGATtCC 121
                                |  120 
                                |   |  
                              115-5CM  
                                  119-TED
   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  (1, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KY8)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: MBD-like (3)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (Q5EFL0_CHICK | Q5EFL0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    5CM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TED  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ky8)
 

(-) 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 - model 1, sites 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
  2ky8
    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 (structure derived) | HSSP (homology derived)
    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
  Q5EFL0_CHICK | Q5EFL0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q5EFL0_CHICK | Q5EFL0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2KY8)

(-) Related Entries Specified in the PDB File

1ig4 MBD1 BOUND TO METHYLATED DNA RELATED ID: 16936 RELATED DB: BMRB
3c2i MECP2 BOUND TO METHYLATED DNA