3DRW Transferase date Jul 11, 2008
title Crystal Structure Of A Phosphofructokinase From Pyrococcus H Ot3 With Amp
authors A.U.Singer, T.Skarina, S.Kochinyan, G.Brown, M.E.Cuff, A.M.Edward A.Joachimiak, A.Savchenko, A.F.Yakunin, Z.Jia, Midwest Center F Structural Genomics (Mcsg)
compound source
Molecule: Adp-Specific Phosphofructokinase
Chain: A, B
Fragment: Phosphofructokinase
Synonym: Adp-Dependent Phosphofructokinase, Adp-Pfk
Ec: 2.7.1.146
Engineered: Yes
Mutation: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Strain: Ot3
Gene: Pfkc, Ph1645
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 1 21 1
R_factor 0.172 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.464 104.190 70.844 90.00 105.09 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand AMP, NA enzyme Transferase E.C.2.7.1.146 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • phosphofructokinase activity...


  • Primary referenceADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645., Currie MA, Merino F, Skarina T, Wong AH, Singer A, Brown G, Savchenko A, Caniuguir A, Guixe V, Yakunin AF, Jia Z, J Biol Chem. 2009 Aug 21;284(34):22664-71. Epub 2009 Jun 24. PMID:19553681
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (3drw.pdb1.gz) 158 Kb
  • LPC: Ligand-Protein Contacts for 3DRW
  • CSU: Contacts of Structural Units for 3DRW
  • Structure Factors (1140 Kb)
  • Retrieve 3DRW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DRW from S2C, [Save to disk]
  • Re-refined 3drw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DRW 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 3DRW
  • 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 3DRW, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3drw_B] [3drw] [3drw_A]
  • SWISS-PROT database: [O59355]
  • Domain organization of [K6PF_PYRHO] by SWISSPFAM
  • Other resources with information on 3DRW
  • Community annotation for 3DRW 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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