1GMO Hormone date Sep 20, 2001
title Crystal Structures Of Nk1-Heparin Complexes Reveal The Basis Activity And Enable Engineering Of Potent Agonists Of The M Receptor
authors D.Lietha, D.Y.Chirgadze, B.Mulloy, T.L.Blundell, E.Gherardi
compound source
Molecule: Hepatocyte Growth Factor
Chain: A, B, C, D, E, F, G, H
Fragment: Nk1
Synonym: Scatter Factor, Sf, Hepatopoeitin A, Hgf
Engineered: Yes
Mutation: Yes
Other_details: Nk1 Dimer In Complex With Heparin Molecule
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Pichia Pastoris
Expression_system_taxid: 644223
Expression_system_strain: Gs115
Expression_system_vector: Yeast
Expression_system_plasmid: Ppic-9k
symmetry Space Group: P 21 21 2
R_factor 0.254 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
179.700 174.100 59.900 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand EPE, IDS, SGN, SO4 enzyme
related structures by homologous chain: 1NK1, 2HGF
Primary referenceCrystal structures of NK1-heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the MET receptor., Lietha D, Chirgadze DY, Mulloy B, Blundell TL, Gherardi E, EMBO J 2001 Oct 15;20(20):5543-55. PMID:11597998
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (1gmo.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (1gmo.pdb2.gz) 63 Kb
  • Biological Unit Coordinates (1gmo.pdb3.gz) 62 Kb
  • Biological Unit Coordinates (1gmo.pdb4.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 1GMO
  • CSU: Contacts of Structural Units for 1GMO
  • Likely Quarternary Molecular Structure file(s) for 1GMO
  • Structure Factors (278 Kb)
  • Retrieve 1GMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GMO from S2C, [Save to disk]
  • Re-refined 1gmo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GMO 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 1GMO
  • 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 1GMO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gmoa2, region A:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoa1, region A:37-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmob2, region B:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gmob1, region B:37-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoc2, region C:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoc1, region C:37-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmod2, region D:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gmod1, region D:37-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoe2, region E:126-209 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoe1, region E:37-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmof2, region F:126-209 [Jmol] [rasmolscript] [script source]
        - Domain d1gmof1, region F:37-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmog2, region G:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gmog1, region G:38-125 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoh2, region H:126-208 [Jmol] [rasmolscript] [script source]
        - Domain d1gmoh1, region H:38-125 [Jmol] [rasmolscript] [script source]
  • Fold representative 1gmo 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: [1gmo_H] [1gmo_G] [1gmo_C] [1gmo_B] [1gmo_D] [1gmo_A] [1gmo_E] [1gmo] [1gmo_F]
  • SWISS-PROT database: [P14210]
  • Domain organization of [HGF_HUMAN] by SWISSPFAM
  • Domains found in 1GMO: [KR] [PAN_AP ] by SMART
  • Other resources with information on 1GMO
  • Community annotation for 1GMO 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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