1QK9 Methyl-Cpg-Binding Protein date Jul 12, 1999
title The Solution Structure Of The Domain From Mecp2 That Binds To Methylated Dna
authors R.I.D.Wakefield, B.O.Smith, X.Nan, A.Free, A.Soteriou, D.Uhrin, A.P.Bird, P.N.Barlow
compound source
Molecule: Methyl-Cpg-Binding Protein 2
Chain: A
Fragment: Mcpg Binding Domain Of Mecp2
Synonym: Mbd
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_cellular_location: Inclusion Bodies
Expression_system_plasmid: Pet6hmbd
methodSolution NMR
related structures by homologous chain: 1UB1
Primary referenceThe solution structure of the domain from MeCP2 that binds to methylated DNA., Wakefield RI, Smith BO, Nan X, Free A, Soteriou A, Uhrin D, Bird AP, Barlow PN, J Mol Biol 1999 Sep 3;291(5):1055-65. PMID:10518942
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (656 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1QK9
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1QK9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QK9 from S2C, [Save to disk]
    • View 1QK9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1QK9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1QK9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qk9a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1qk9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1qk9_A]
  • SWISS-PROT database: [P51608]
  • Domain organization of [MECP2_HUMAN] by SWISSPFAM
  • Domain found in 1QK9: [MBD ] by SMART
  • Alignments of the sequence of 1QK9 with the sequences similar proteins can be viewed for 1QK9's classification [MECP2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [MECP2_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1QK9
  • Community annotation for 1QK9 at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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