5CS9 Hormone date Jul 23, 2015
title The Structure Of The Nk1 Fragment Of Hgfsf Complexed With M
authors A.G.Sigurdardottir, A.Winter, A.Sobkowicz, M.Fragai, D.Y.Chirgad D.B.Ascher, T.L.Blundell, E.Gherardi
compound source
Molecule: Hepatocyte Growth Factor
Chain: A, B
Fragment: Unp Residues 28-210
Synonym: Hepatopoietin-A,Scatter Factor,Sf
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hgf, Hpta
Expression_system: Komagataella Pastoris Cbs 7435
Expression_system_taxid: 981350
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.286 64.152 57.199 90.00 94.96 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EDO, MES enzyme
Primary referenceExploring the chemical space of the lysine-binding pocket of the first kringle domain of hepatocyte growth factor/scatter factor (HGF/SF) yields a new class of inhibitors of HGF/SF-MET binding., Sigurdardottir AG, Winter A, Sobkowicz A, Fragai M, Chirgadze D, Ascher DB, Blundell TL, Gherardi E, Chem Sci. 2015 Nov 1;6(11):6147-6157. doi: 10.1039/c5sc02155c. Epub 2015 Jul 31. PMID:30090230
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (5cs9.pdb1.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 5CS9
  • CSU: Contacts of Structural Units for 5CS9
  • Structure Factors (470 Kb)
  • Retrieve 5CS9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CS9 from S2C, [Save to disk]
  • Re-refined 5cs9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cs9_A] [5cs9_B] [5cs9]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CS9: [KR] [PAN_AP ] by SMART
    • Other resources with information on 5CS9
  • Community annotation for 5CS9 at PDBWiki (http://pdbwiki.org)

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