5VMZ	Transcription Dna	date	Apr 28, 2017
title	Kaiso (Zbtb33) E535q Mutant Zinc Finger Dna Binding Domain I With A Double Cpg-Methylated Dna Resembling The Specific Ka Binding Sequence (Kbs)
authors	E.N.Nikolova, R.L.Stanfield, M.A.Martinez-Yamout, H.J.Dyson, P.E
compound		source
Molecule: Transcriptional Regulator Kaiso Chain: A Synonym: Zinc Finger And Btb Domain-Containing Protein 33 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Zbtb33, Kaiso, Znf348 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) [Dnay] Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21d
Molecule: Dna (5'-D(Tpgpcptptpcpcp(5cm)Pgp(5cm) Pgpapaptpapapcpg)-3'); Chain: D Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna (5'-D(Cpgptptpaptptp(5cm)Pgp(5cm) Pgpgpgpapapgpcpa)-3'); Chain: E Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: C 2 2 2	R_factor 0.167 R_Free 0.199
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.409 183.487 104.003 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.32 Å
ligand	5CM, CL, TLA, ZN	enzyme
Primary reference	CH...O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso., Nikolova EN, Stanfield RL, Dyson HJ, Wright PE, Biochemistry. 2018 Mar 26. doi: 10.1021/acs.biochem.8b00065. PMID:29546986

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk] Biological Unit Coordinates (5vmz.pdb1.gz) 79 Kb LPC: Ligand-Protein Contacts for 5VMZ CSU: Contacts of Structural Units for 5VMZ Structure Factors (256 Kb) Retrieve 5VMZ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5VMZ from S2C, [Save to disk]

View 5VMZ 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 5VMZ

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5vmz_E] [5vmz_A] [5vmz_D] SWISS-PROT database: Domain organization of by SWISSPFAM

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Community annotation for 5VMZ at PDBWiki (http://pdbwiki.org)

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