1GP9 Hormone Growth Factor date Oct 31, 2001
title A New Crystal Form Of The Nk1 Splice Variant Of Hgfsf Demon Extensive Hinge Movement And Suggests That The Nk1 Dimer Or By Domain Swapping
authors K.Watanabe, D.Y.Chirgadze, D.Lietha, E.Gherardi, T.L.Blundell
compound source
Molecule: Hepatocyte Growth Factor
Chain: A, B, C, D
Fragment: Nk1, Residues 40-210
Synonym: Scatter Factor, Sf, Hepatopoeitin A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Fibroblast
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_variant: Gs115
Expression_system_vector: Ppic-9k
Expression_system_plasmid: Ppic-9k
symmetry Space Group: C 2 2 21
R_factor 0.237 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.480 78.260 304.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand EPE enzyme
related structures by homologous chain: 1GMN, 1NK1
Primary referenceA new crystal form of the NK1 splice variant of HGF/SF demonstrates extensive hinge movement and suggests that the NK1 dimer originates by domain swapping., Watanabe K, Chirgadze DY, Lietha D, de Jonge H, Blundell TL, Gherardi E, J Mol Biol 2002 May 31;319(2):283-8. PMID:12051906
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (1gp9.pdb1.gz) 59 Kb
  • Biological Unit Coordinates (1gp9.pdb2.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 1GP9
  • CSU: Contacts of Structural Units for 1GP9
  • Likely Quarternary Molecular Structure file(s) for 1GP9
  • Structure Factors (246 Kb)
  • Retrieve 1GP9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GP9 from S2C, [Save to disk]
  • Re-refined 1gp9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GP9 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 1GP9
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1GP9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gp9a2, region A:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9a1, region A:39-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9b2, region B:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9b1, region B:39-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9c2, region C:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9c1, region C:38-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9d2, region D:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gp9d1, region D:39-125 [Jmol] [rasmolscript] [script source]
  • Fold representative 1gp9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1gp9_C] [1gp9] [1gp9_D] [1gp9_B] [1gp9_A]
  • SWISS-PROT database: [P14210]
  • Domain organization of [HGF_HUMAN] by SWISSPFAM
  • Domains found in 1GP9: [KR] [PAN_AP ] by SMART
  • Other resources with information on 1GP9
  • Community annotation for 1GP9 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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