6CCG Transcription date Feb 07, 2018
title Crystal Structure Mbd3 Mbd Domain In Complex With Methylated
authors K.Liu, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, St Genomics Consortium (Sgc)
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 3
Chain: A, B
Fragment: Residues 1-71
Synonym: Methyl-Cpg-Binding Protein Mbd3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-V2r-Prare2
Expression_system_plasmid: Pet28-Gstlic

Molecule: Dna
Chain: C, D, E, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Dna Construct
symmetry Space Group: C 1 2 1
R_factor 0.223 R_Free 0.250
length a length b length c angle alpha angle beta angle gamma
72.270 36.460 130.840 90.00 92.42 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 5CM, UNX enzyme
A, B

Primary referenceStructural analyses reveal that MBD3 is a methylated CG binder., Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J, FEBS J. 2019 Apr 13. doi: 10.1111/febs.14850. PMID:30980593
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (6ccg.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (6ccg.pdb2.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 6CCG
  • CSU: Contacts of Structural Units for 6CCG
  • Structure Factors (3072 Kb)
  • Retrieve 6CCG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CCG from S2C, [Save to disk]
  • View 6CCG 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 6CCG
  • 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 6ccg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ccg_F] [6ccg_A] [6ccg_C] [6ccg_D] [6ccg_B] [6ccg_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CCG
  • Community annotation for 6CCG at PDBWiki (http://pdbwiki.org)

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