2GFA Metal Binding Protein date Mar 21, 2006
title Double Tudor Domain Complex Structure
authors Y.Huang, J.Fang, M.T.Bedford, Y.Zhang, R.M.Xu
compound source
Molecule: Jumonji Domain-Containing Protein 2a
Chain: A, B
Fragment: Double Tudor Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jmjd2a, Jmjd2, Kiaa0677
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Peptide
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occrus Naturally In Humans
symmetry Space Group: C 2 2 21
R_factor 0.224 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.822 96.733 110.057 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand M3L enzyme
Primary referenceRecognition of Histone H3 Lysine-4 Methylation by the Double Tudor Domain of JMJD2A., Huang Y, Fang J, Bedford MT, Zhang Y, Xu RM, Science. 2006 Apr 6;. PMID:16601153
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (2gfa.pdb1.gz) 21 Kb
  • Biological Unit Coordinates (2gfa.pdb2.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 2GFA
  • CSU: Contacts of Structural Units for 2GFA
  • Likely Quarternary Molecular Structure file(s) for 2GFA
  • Structure Factors (306 Kb)
  • Retrieve 2GFA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GFA from S2C, [Save to disk]
  • Re-refined 2gfa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2GFA 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 2GFA
  • 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
  • 3D motif for 2GFA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gfa_C] [2gfa_D] [2gfa] [2gfa_B] [2gfa_A]
  • SWISS-PROT database: [O75164]
  • Domain organization of [KDM4A_HUMAN] by SWISSPFAM
  • Domain found in 2GFA: [TUDOR ] by SMART
  • Other resources with information on 2GFA
  • Community annotation for 2GFA 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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