3RKQ Transcription Dna date Apr 18, 2011
title Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
authors C.Genis, P.Scone, H.Kasahara, H.J.Nam
compound source
Molecule: Homeobox Protein Nkx-2.5
Chain: A, B
Fragment: Homeodomain, Unp Residues 138-194
Synonym: Cardiac-Specific Homeobox, Homeobox Protein Csx, H Protein Nk-2 Homolog E;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nkx2-5, Csx, Nkx2.5, Nkx2e
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Anf-242 Dna
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Anf-242 Dna
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 65
R_factor 0.211 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.450 71.450 94.330 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the human NKX2.5 homeodomain in complex with DNA target., Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ, Biochemistry. 2012 Aug 14;51(32):6312-9. Epub 2012 Aug 3. PMID:22849347
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (3rkq.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3RKQ
  • CSU: Contacts of Structural Units for 3RKQ
  • Structure Factors (215 Kb)
  • Retrieve 3RKQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RKQ from S2C, [Save to disk]
  • Re-refined 3rkq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RKQ 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 3RKQ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3RKQ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rkq_D] [3rkq_A] [3rkq_B] [3rkq_C] [3rkq]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3RKQ: [HOX ] by SMART
  • Other resources with information on 3RKQ
  • Community annotation for 3RKQ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science