1IG4 Transcription Dna date Apr 17, 2001
title Solution Structure Of The Methyl-Cpg-Binding Domain Of Human Mbd1 In Complex With Methylated Dna
authors I.Ohki, N.Shimotake, N.Fujita, J.G.Jee, T.Ikegami, M.Nakao, M.Shirakawa
compound source
Molecule: Methyl-Cpg Binding Protein
Chain: A
Fragment: Methyl-Cpg-Binding Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t

Molecule: 5'-D(Gptpaptpcp(5cm)Pgpgpaptpapc)-3'
Chain: B, C
Engineered: Yes

Synthetic: Yes
methodSolution NMR
ligand 5CM enzyme
related structures by homologous chain: 1D9N

Primary referenceSolution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA., Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, Shirakawa M, Cell 2001 May 18;105(4):487-97. PMID:11371345
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (661 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 1IG4
  • CSU: Contacts of Structural Units for 1IG4
  • Retrieve 1IG4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IG4 from S2C, [Save to disk]
  • View 1IG4 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 1IG4
  • 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 1IG4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ig4a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1ig4 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: [1ig4_C] [1ig4_B] [1ig4_A] [1ig4]
  • SWISS-PROT database: [Q9UIS9]
  • Domain organization of [MBD1_HUMAN] by SWISSPFAM
  • Domain found in 1IG4: [MBD ] by SMART
  • Other resources with information on 1IG4
  • Community annotation for 1IG4 at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1IG4 from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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