4O64 Metal Binding Protein date Dec 20, 2013
title Zinc Fingers Of Kdm2b
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: Lysine-Specific Demethylase 2b
Chain: A, B, C
Fragment: Unp Residues 607-723
Synonym: Cxxc-Type Zinc Finger Protein 2, F-Box And Leucine Repeat Protein 10, F-Box Protein Fbl10, F-Boxlrr-Repeat Pr Jmjc Domain-Containing Histone Demethylation Protein 1b, Ju Domain-Containing Emsy-Interactor Methyltransferase Motif P Protein Jemma, Protein-Containing Cxxc Domain 2, [Histone-H 36 Demethylase 1b;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm2b, Cxxc2, Fbl10, Fbxl10, Jhdm1b, Pccx2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-V2r-Prare2
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 31
R_factor 0.191 R_Free 0.220
length a length b length c angle alpha angle beta angle gamma
107.322 107.322 34.130 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.13 Å
ligand UNX, ZN enzyme
A, C, 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] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (4o64.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (4o64.pdb2.gz) 39 Kb
  • Biological Unit Coordinates (4o64.pdb3.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 4O64
  • CSU: Contacts of Structural Units for 4O64
  • Structure Factors (1434 Kb)
  • Retrieve 4O64 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4O64 from S2C, [Save to disk]
  • Re-refined 4o64 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4O64 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 4O64
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4O64, from MSDmotif at EBI
  • Fold representative 4o64 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4o64] [4o64_A] [4o64_B] [4o64_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4O64: [PHD ] by SMART
  • Other resources with information on 4O64
  • Community annotation for 4O64 at PDBWiki (http://pdbwiki.org)

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