5W9Q Dna Binding Protein Dna date Jun 23, 2017
title Zinc Finger Region Of Mbd1 In Complex With Cpg Dna
authors K.Liu, C.Xu, W.Tempel, J.R.Walker, C.H.Arrowsmith, C.Bountra, A.M. J.Min, Structural Genomics Consortium (Sgc)
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 1
Chain: A, B
Fragment: Zinc Finger Region (Unp Residues 330-388)
Synonym: Cxxc-Type Zinc Finger Protein 3,Methyl-Cpg-Binding Mbd1,Protein Containing Methyl-Cpg-Binding Domain 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd1, Cxxc3, Pcm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-V2r-Prare2
Expression_system_plasmid: Pet28-Mhl

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.226 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
139.339 27.800 64.914 90.00 106.52 90.00
method X-Ray Diffractionresolution 1.80 Å
A, B

Primary referenceDNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants., Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J, Structure. 2017 Dec 16. pii: S0969-2126(17)30396-9. doi:, 10.1016/j.str.2017.11.022. PMID:29276034
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (5w9q.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (5w9q.pdb2.gz) 40 Kb
  • CSU: Contacts of Structural Units for 5W9Q
  • Structure Factors (2108 Kb)
  • Retrieve 5W9Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5W9Q from S2C, [Save to disk]
  • View 5W9Q 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 5W9Q
  • 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 5w9q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5w9q_F] [5w9q_B] [5w9q_E] [5w9q_D] [5w9q_C] [5w9q_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5W9Q
  • Community annotation for 5W9Q at PDBWiki (http://pdbwiki.org)

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