6C1A Dna Binding Protein Dna date Jan 04, 2018
title Mbd2 In Complex With Methylated Dna
authors K.Liu, C.Xu, W.Tempel, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.M Structural Genomics Consortium (Sgc)
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 2
Chain: A, B, E, F
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-Prare2
Expression_system_plasmid: Pet28-Mhl

Molecule: Dna Strand 1
Chain: C, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic

Molecule: Complement To Dna Strand 1
Chain: D, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic
symmetry Space Group: P 1
R_factor 0.231 R_Free 0.265
length a length b length c angle alpha angle beta angle gamma
36.533 39.875 105.151 83.97 85.70 62.75
method X-Ray Diffractionresolution 2.05 Å
ligand 5CM, UNX enzyme
F, A, E, B

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] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (6c1a.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (6c1a.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 6C1A
  • CSU: Contacts of Structural Units for 6C1A
  • Structure Factors (2173 Kb)
  • Retrieve 6C1A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6C1A from S2C, [Save to disk]
  • View 6C1A 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 6C1A
  • 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 6c1a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6c1a_D] [6c1a_B] [6c1a_G] [6c1a_H] [6c1a_F] [6c1a_C] [6c1a_E] [6c1a_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6C1A
  • Community annotation for 6C1A at PDBWiki (http://pdbwiki.org)

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