1D9N Gene Regulation date Oct 28, 1999
title Solution Structure Of The Methyl-Cpg-Binding Domain Of The Methylation-Dependent Transcriptional Repressor Mbd1pcm1
authors I.Ohki, N.Shimotake, N.Fujita, M.Nakao, M.Shirakawa
compound source
Molecule: Methyl-Cpg-Binding Protein Mbd1
Chain: A
Fragment: Methyl-Cpg-Binding Domain Of Mbd1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a
Expression_system_plasmid: Pgex-2t
methodSolution NMR
related structures by homologous chain: 1IG4

Primary referenceSolution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1., Ohki I, Shimotake N, Fujita N, Nakao M, Shirakawa M, EMBO J 1999 Dec 1;18(23):6653-61. PMID:10581239
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (500 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1D9N
  • Retrieve 1D9N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D9N from S2C, [Save to disk]
  • View 1D9N 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.
  • Visual 3D analysis of 1D9N
  • 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 1D9N, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d9na_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1d9n 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: [1d9n] [1d9n_A]
  • SWISS-PROT database: [Q9UIS9]
  • Domain organization of [MBD1_HUMAN] by SWISSPFAM
  • Domain found in 1D9N: [MBD ] by SMART
  • Other resources with information on 1D9N
  • Community annotation for 1D9N 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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