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- PDB-4d3c: Crystal structure of the NK1 domain of HGF in complex with anti-H... -

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Basic information

Entry
Database: PDB / ID: 4d3c
TitleCrystal structure of the NK1 domain of HGF in complex with anti-HGF monoclonal antibody SFN68.
Components
  • (SFN68 FAB) x 2
  • HEPATOCYTE GROWTH FACTOR
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


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 / MET receptor recycling / cellular response to hepatocyte growth factor stimulus / MET activates PTPN11 / hepatocyte growth factor receptor signaling pathway ...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 / MET receptor recycling / cellular response to hepatocyte growth factor stimulus / MET activates PTPN11 / hepatocyte growth factor receptor signaling pathway / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / positive regulation of osteoblast differentiation / epithelial to mesenchymal transition / immunoglobulin complex / MET activates RAS signaling / platelet alpha granule lumen / negative regulation of autophagy / Interleukin-7 signaling / growth factor activity / cell chemotaxis / Negative regulation of MET activity / 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 / adaptive immune response / 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 region / membrane / identical protein binding
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / : ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Plasminogen Kringle 4 / Plasminogen Kringle 4 / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKang, Y.J. / Kim, K.L. / Cho, H.S. / Chung, J.H.
CitationJournal: to be published
Title: A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist.
Authors: Kang, Y.J. / Kim, K.L. / Cho, H.S. / Chung, J.H.
History
DepositionOct 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.journal_abbrev / _citation.title
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEPATOCYTE GROWTH FACTOR
H: SFN68 FAB
L: SFN68 FAB


Theoretical massNumber of molelcules
Total (without water)68,4483
Polymers68,4483
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-29.6 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.703, 297.692, 70.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HEPATOCYTE GROWTH FACTOR / HEPATOPOIETIN-A / SCATTER FACTOR / SF / NK1


Mass: 22242.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-210 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14210
#2: Antibody SFN68 FAB


Mass: 23230.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RABBIT/HUMAN CHIMERIC ANTIBODY / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#3: Antibody SFN68 FAB


Mass: 22974.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RABBIT/HUMAN CHIMERIC ANTIBODY / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: U3KM01*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Type: PAL/PLS / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.62→29.79 Å / Num. obs: 25541 / % possible obs: 95.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JPT, 1NK1.

1jpt

1nk1


Resolution: 2.62→29.79 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.56 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.511 / ESU R Free: 0.328 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.29758 1347 5 %
Rwork0.2676 --
obs0.26913 25541 95.51 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.704 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.01 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.62→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 0 22 4247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024329
X-RAY DIFFRACTIONr_bond_other_d0.0070.023967
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.955882
X-RAY DIFFRACTIONr_angle_other_deg0.8353.0049161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4924.36172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56315691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6111517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214910
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02977
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.618→2.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 92 -
Rwork0.396 1586 -
obs--82.58 %

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