1NGN Dna Binding Protein date Dec 17, 2002
title Mismatch Repair In Methylated Dna. Structure Of The Mismatch Thymine Glycosylase Domain Of Methyl-Cpg-Binding Protein Mb
authors P.Wu, C.Qiu, A.Sohail, X.Zhang, A.S.Bhagwat, X.Cheng
compound source
Molecule: Methyl-Cpg Binding Protein Mbd4
Chain: A
Fragment: Glycosylase Domain
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Mbd4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Modified Pet28b
symmetry Space Group: P 31 2 1
R_factor 0.213 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.580 48.580 146.570 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4., Wu P, Qiu C, Sohail A, Zhang X, Bhagwat AS, Cheng X, J Biol Chem 2003 Feb 14;278(7):5285-91. PMID:12456671
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (1ngn.pdb1.gz) 26 Kb
  • CSU: Contacts of Structural Units for 1NGN
  • Likely Quarternary Molecular Structure file(s) for 1NGN
  • Retrieve 1NGN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NGN from S2C, [Save to disk]
    • View 1NGN 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 1NGN
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NGN, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ngna_, region A [Jmol] [rasmolscript] [script source]
  • 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: [1ngn] [1ngn_A]
  • SWISS-PROT database: [Q9Z2D7]
  • Domain organization of [MBD4_MOUSE] by SWISSPFAM
    • Other resources with information on 1NGN
  • Community annotation for 1NGN at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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