1YV5 Transferase date Feb 15, 2005
title Human Farnesyl Diphosphate Synthase Complexed With Mg And Ri
authors K.L.Kavanagh, K.Guo, F.Von Delft, C.Arrowsmith, M.Sundstrom, A.Ed U.Oppermann, Structural Genomics Consortium (Sgc)
compound source
Molecule: Farnesyl Pyrophosphate Synthetase
Chain: A
Synonym: Fpp Synthetase, Fps, Farnesyl Diphosphate Syntheta Geranyltranstransferase;
Ec: 2.5.1.10
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fdps
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11 Derivative
symmetry Space Group: P 41 21 2
R_factor 0.205 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.946 110.946 70.264 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MG, PO4, RIS BindingDB enzyme Transferase E.C.2.5.1.10 BRENDA
related structures by homologous chain: 1YQ7
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs., Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U, Proc Natl Acad Sci U S A. 2006 May 16;103(20):7829-34. Epub 2006 May 9. PMID:16684881
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (1yv5.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 1YV5
  • CSU: Contacts of Structural Units for 1YV5
  • Likely Quarternary Molecular Structure file(s) for 1YV5
  • Structure Factors (222 Kb)
  • Retrieve 1YV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YV5 from S2C, [Save to disk]
  • Re-refined 1yv5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YV5 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 1YV5
  • 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 1YV5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yv5_A] [1yv5]
  • SWISS-PROT database: [P14324]
  • Domain organization of [FPPS_HUMAN] by SWISSPFAM
  • Other resources with information on 1YV5
  • Community annotation for 1YV5 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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