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- PDB-2hgf: HAIRPIN LOOP CONTAINING DOMAIN OF HEPATOCYTE GROWTH FACTOR, NMR, ... -

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Basic information

Entry
Database: PDB / ID: 2hgf
TitleHAIRPIN LOOP CONTAINING DOMAIN OF HEPATOCYTE GROWTH FACTOR, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsHEPATOCYTE GROWTH FACTOR
KeywordsHEPATOCYTE GROWTH FACTOR / SCATTER FACTOR / HAIRPIN LOOP / HEPARIN BINDING / PLASMINOGEN RELATED / NK1
Function / homology
Function and homology information


regulation of p38MAPK cascade / skeletal muscle cell proliferation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / skeletal muscle cell proliferation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / myoblast proliferation / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-7 signaling / negative regulation of autophagy / platelet alpha granule lumen / epithelial cell proliferation / cell chemotaxis / growth factor activity / liver development / Negative regulation of MET activity / negative regulation of inflammatory response / cell morphogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / Platelet degranulation / PIP3 activates AKT signaling / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / signaling receptor binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 3-Layer(bba) Sandwich / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE-GEOMETRY SIMULATED ANNEALING
AuthorsZhou, H. / Mazzulla, M.J. / Kaufman, J.D. / Stahl, S.J. / Wingfield, P.T. / Rubin, J.S. / Bottaro, D.P. / Byrd, R.A.
Citation
Journal: Structure / Year: 1998
Title: The solution structure of the N-terminal domain of hepatocyte growth factor reveals a potential heparin-binding site.
Authors: Zhou, H. / Mazzulla, M.J. / Kaufman, J.D. / Stahl, S.J. / Wingfield, P.T. / Rubin, J.S. / Bottaro, D.P. / Byrd, R.A.
#1: Journal: Biochem.J. / Year: 1997
Title: Functional and Biophysical Characterization of Recombinant Human Hepatocyte Growth Factor Isoforms Produced in Escherichia Coli
Authors: Stahl, S.J. / Wingfield, P.T. / Kaufman, J.D. / Pannell, L.K. / Cioce, V. / Sakata, H. / Taylor, W.G. / Rubin, J.S. / Bottaro, D.P.
History
DepositionDec 18, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEPATOCYTE GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)11,4011
Polymers11,4011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 60RESTRAINED, MINIMIZED MEAN STRUCTURE
Representative

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Components

#1: Protein HEPATOCYTE GROWTH FACTOR / HGF/N


Mass: 11401.286 Da / Num. of mol.: 1 / Fragment: AMINO TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P14210
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE REFERENCE.

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
X-PLOR3.8structure solution
RefinementMethod: DISTANCE-GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: RESTRAINED, MINIMIZED MEAN STRUCTURE
Conformers calculated total number: 60 / Conformers submitted total number: 1

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