3PTR Protein Binding date Dec 03, 2010
title Phf2 Jumonji Domain
authors J.R.Horton, A.K.Upadhyay, H.Hashimoto, X.Zhang, X.Cheng
compound source
Molecule: Phd Finger Protein 2
Chain: B
Fragment: Jumonji Domain (Unp Residues 60-451)
Synonym: Grc5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Phf2, Kiaa0662
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pxc870
symmetry Space Group: P 21 21 21
R_factor 0.180 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.737 66.512 104.567 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand EDO enzyme
Primary referenceStructural Basis for Human PHF2 Jumonji Domain Interaction with Metal Ions., Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X, J Mol Biol. 2010 Dec 15. PMID:21167174
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (3ptr.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 3PTR
  • CSU: Contacts of Structural Units for 3PTR
  • Structure Factors (463 Kb)
  • Retrieve 3PTR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PTR from S2C, [Save to disk]
  • Re-refined 3ptr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PTR 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 3PTR
  • 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 3PTR, from MSDmotif at EBI
  • Fold representative 3ptr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ptr_B] [3ptr]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PTR: [JmjC ] by SMART
  • Other resources with information on 3PTR
  • Community annotation for 3PTR 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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