2MOE Hydrolase Dna date Apr 24, 2014
title Solution Structure Of Mbd4 Methyl-Cytosine Binding Domain Bo Methylated Dna
authors D.C.Williams, N.M.Walavalkar
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 4
Chain: A
Fragment: Unp Residues 80-148
Synonym: Methyl-Cpg-Binding Endonuclease 1, Methyl-Cpg-Bind Protein Mbd4, Mismatch-Specific Dna N-Glycosylase;
Ec: 3.2.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd4, Med1

Molecule: Dna (5'-D(Gpgpaptp(5cm)Pgpgpcptpc)-3')
Chain: B
Engineered: Yes
Other_details: Mbd4mbd

Synthetic: Yes

Molecule: Dna (5'-D(Gpapgpcp(5cm)Pgpaptpcpc)-3')
Chain: C
Engineered: Yes
Other_details: Dnarev

Synthetic: Yes
methodSolution NMR
ligand 5CM enzyme Hydrolase E.C.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSolution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches., Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN, Williams DC Jr, Nucleic Acids Res. 2014;42(17):11218-32. doi: 10.1093/nar/gku782. Epub 2014 Sep, 2. PMID:25183517
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (609 Kb) [Save to disk]
  • Biological Unit Coordinates (2moe.pdb1.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 2MOE
  • CSU: Contacts of Structural Units for 2MOE
  • Original NMR restraints for 2MOE from PDB
  • Retrieve 2MOE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2MOE from S2C, [Save to disk]
  • View 2MOE 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 2MOE
  • 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 2MOE, from MSDmotif at EBI
  • Fold representative 2moe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2moe_A] [2moe] [2moe_C] [2moe_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2MOE: [MBD ] by SMART
  • Other resources with information on 2MOE
  • Community annotation for 2MOE at PDBWiki (http://pdbwiki.org)

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