2H1K Transcription Dna date May 16, 2006
title Crystal Structure Of The Pdx1 Homeodomain In Complex With Dn
authors A.Longo, G.P.Guanga, R.B.Rose
compound source
Molecule: 15-Mer Dna
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: 15-Mer Dna
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Pancreatic And Duodenal Homeobox 1
Chain: A, B
Fragment: Residues 146-206
Synonym: Insulin Promoter Factor 1; Ipf-1; Homeodomain Prot
Engineered: Yes

Organism_scientific: Mesocricetus Auratus
Organism_common: Golden Hamster
Organism_taxid: 10036
Gene: Ipf1, Pdx1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: P 21 21 21
R_factor 0.227 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.282 61.928 96.445 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.42 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for induced fit mechanisms in DNA recognition by the pdx1 homeodomain(,)., Longo A, Guanga GP, Rose RB, Biochemistry. 2007 Mar 20;46(11):2948-57. Epub 2007 Feb 23. PMID:17315980
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (2h1k.pdb1.gz) 23 Kb
  • Biological Unit Coordinates (2h1k.pdb2.gz) 23 Kb
  • CSU: Contacts of Structural Units for 2H1K
  • Likely Quarternary Molecular Structure file(s) for 2H1K
  • Structure Factors (111 Kb)
  • Retrieve 2H1K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H1K from S2C, [Save to disk]
  • Re-refined 2h1k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H1K 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 2H1K
  • 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 2H1K, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h1k_E] [2h1k_B] [2h1k] [2h1k_D] [2h1k_F] [2h1k_C] [2h1k_A]
  • SWISS-PROT database: [P70118]
  • Domain organization of [PDX1_MESAU] by SWISSPFAM
  • Domain found in 2H1K: [HOX ] by SMART
  • Other resources with information on 2H1K
  • Community annotation for 2H1K 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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