1NK1 Hormone Growth Factor date Aug 20, 1998
title Nk1 Fragment Of Human Hepatocyte Growth Factorscatter Factor (Hgfsf) At 2.5 Angstrom Resolution
authors D.Y.Chirgadze, J.P.Hepple, H.Zhou, R.A.Byrd, T.L.Blundell, E.Gherardi
compound source
Molecule: Protein (Hepatocyte Growth Factor Precursor)
Chain: A, B
Fragment: Nk1
Synonym: Scatter Factor, Sf, Hepatopoeitin A
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Mrc5
Organ: Lung
Cell: Fibroblast
Cellular_location: Extracellular
Gene: Hepatocyte Growth Factorscatter Factor
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Gs115
Expression_system_cellular_location: Extracellular
Expression_system_vector_type: Plasmid
Expression_system_vector: Yeast
Expression_system_plasmid: Ppic-9k
Expression_system_gene: Aox-1
Other_details: Synthetic Gene
symmetry Space Group: P 1 21 1
R_factor 0.245 R_Free 0.319
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.420 63.560 56.810 90.00 96.04 90.00
method X-Ray Diffractionresolution 2.50 Å
related structures by homologous chain: 1GMO, 1GP9
Primary referenceCrystal structure of the NK1 fragment of HGF/SF suggests a novel mode for growth factor dimerization and receptor binding., Chirgadze DY, Hepple JP, Zhou H, Byrd RA, Blundell TL, Gherardi E, Nat Struct Biol 1999 Jan;6(1):72-9. PMID:9886295
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (1nk1.pdb1.gz) 58 Kb
  • CSU: Contacts of Structural Units for 1NK1
  • Likely Quarternary Molecular Structure file(s) for 1NK1
  • Structure Factors (199 Kb)
  • Retrieve 1NK1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NK1 from S2C, [Save to disk]
  • Re-refined 1nk1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NK1 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 1NK1
  • 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 1NK1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nk1a2, region A:126-209 [Jmol] [rasmolscript] [script source]
        - Domain d1nk1a1, region A:38-125 [Jmol] [rasmolscript] [script source]
        - Domain d1nk1b2, region B:126-209 [Jmol] [rasmolscript] [script source]
        - Domain d1nk1b1, region B:38-125 [Jmol] [rasmolscript] [script source]
  • Fold representative 1nk1 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: [1nk1_B] [1nk1_A] [1nk1]
  • SWISS-PROT database: [P14210]
  • Domain organization of [HGF_HUMAN] by SWISSPFAM
  • Domains found in 1NK1: [KR] [PAN_AP ] by SMART
  • Alignments of the sequence of 1NK1 with the sequences similar proteins can be viewed for 1NK1's classification [HGF_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [HGF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1NK1
  • Community annotation for 1NK1 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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