3KQI Nuclear Protein date Nov 17, 2009
title Crystal Structure Of Phf2 Phd Domain Complexed With H3k4me3
authors H.Wen, J.Z.Li, T.Song, M.Lu, M.Lee
compound source
Molecule: Phd Finger Protein 2
Chain: A
Fragment: Phd Finger
Synonym: Grc5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kiaa0662, Phf2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p1

Molecule: H3k4me3 Peptide
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 65 2 2
R_factor 0.190 R_Free 0.218
length a length b length c angle alpha angle beta angle gamma
77.757 77.758 72.116 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.78 Å
ligand CL, GOL, M3L, MG, ZN enzyme
Primary referenceRecognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation., Wen H, Li J, Song T, Lu M, Kan PY, Lee MG, Sha B, Shi X, J Biol Chem. 2010 Mar 26;285(13):9322-6. Epub 2010 Feb 2. PMID:20129925
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (22 Kb) [Save to disk]
  • Biological Unit Coordinates (3kqi.pdb1.gz) 16 Kb
  • Biological Unit Coordinates (3kqi.pdb2.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 3KQI
  • CSU: Contacts of Structural Units for 3KQI
  • Structure Factors (97 Kb)
  • Retrieve 3KQI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KQI from S2C, [Save to disk]
  • Re-refined 3kqi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KQI 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 3KQI
  • 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 3KQI, from MSDmotif at EBI
  • Fold representative 3kqi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kqi] [3kqi_B] [3kqi_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KQI: [PHD ] by SMART
  • Other resources with information on 3KQI
  • Community annotation for 3KQI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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