6C1T Dna Binding Protein Dna date Jan 05, 2018
title Mbd2 In Complex With A Partially Methylated Dna
authors M.Lei, W.Tempel, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.Min, St Genomics Consortium (Sgc)
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 2
Chain: A, D
Synonym: Demethylase,Dmtase,Methyl-Cpg-Binding Protein Mbd2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-V2r-Ril
Expression_system_plasmid: Pet28-Mhl

Molecule: 12-Mer Dna
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 12-Mer Dna
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.214 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
71.473 36.933 104.076 90.00 108.25 90.00
method X-Ray Diffractionresolution 1.84 Å
ligand 5CM, GOL, SO4, UNX enzyme
A, D

Primary referenceStructural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA., Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J, J Biol Chem. 2018 Mar 22. pii: RA118.001785. doi: 10.1074/jbc.RA118.001785. PMID:29567833
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (6c1t.pdb1.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 6C1T
  • CSU: Contacts of Structural Units for 6C1T
  • Structure Factors (1747 Kb)
  • Retrieve 6C1T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6C1T from S2C, [Save to disk]
  • View 6C1T 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 6C1T
  • 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
  • Fold representative 6c1t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6c1t_B] [6c1t_C] [6c1t_A] [6c1t_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6C1T
  • Community annotation for 6C1T at PDBWiki (http://pdbwiki.org)

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