2KGI Metal Binding Protein date Mar 12, 2009
title Solution Structure Of Jarid1a C-Terminal Phd Finger In Compl H3(1-9)K4me3
authors J.Song, Z.Wang, D.J.Patel
compound source
Molecule: Histone Demethylase Jarid1a
Chain: A
Fragment: Phd-Type C-Terminal Zinc Finger
Synonym: Jumonjiarid Domain-Containing Protein 1a, Retinob Binding Protein 2, Rbbp-2;
Ec: 1.14.11.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jarid1a, Rbbp2, Rbp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1

Molecule: H3(1-9)K4me3
Chain: B
Engineered: Yes
Synthetic: Yes
methodSolution NMR
ligand M3L, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceHaematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger., Wang GG, Song J, Wang Z, Dormann HL, Casadio F, Li H, Luo JL, Patel DJ, Allis CD, Nature. 2009 May 10. PMID:19430464
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (307 Kb) [Save to disk]
  • Biological Unit Coordinates (2kgi.pdb1.gz) 16 Kb
  • LPC: Ligand-Protein Contacts for 2KGI
  • CSU: Contacts of Structural Units for 2KGI
  • Original NMR restraints for 2KGI from PDB
  • Retrieve 2KGI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2KGI from S2C, [Save to disk]
    • View 2KGI 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 2KGI
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2KGI, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2kgi_B] [2kgi_A] [2kgi]
  • SWISS-PROT database: [P29375]
  • Domain organization of [KDM5A_HUMAN] by SWISSPFAM
  • Domain found in 2KGI: [PHD ] by SMART
    • Other resources with information on 2KGI
  • Community annotation for 2KGI 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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