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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 / homologyImmunoglobulin C1-set domain / Hepatocyte growth factor / Kringle, conserved site / Kringle domain signature. / Immunoglobulin V-set domain / Trypsin / Kringle domain / PAN domain / Kringle superfamily / Immunoglobulin-like domain superfamily ...Immunoglobulin C1-set domain / Hepatocyte growth factor / Kringle, conserved site / Kringle domain signature. / Immunoglobulin V-set domain / Trypsin / Kringle domain / PAN domain / Kringle superfamily / Immunoglobulin-like domain superfamily / Hepatocyte growth factor-like / Ig-like domain profile. / Kringle / Serine proteases, trypsin domain / Peptidase S1A, chymotrypsin family / Immunoglobulin subtype / PAN/Apple domain / Immunoglobulin-like domain / Peptidase S1, PA clan / Immunoglobulin V-set domain / Immunoglobulin-like fold / Serine proteases, trypsin domain profile. / Kringle domain profile. / Kringle-like fold / RAF/MAP kinase cascade / MET activates STAT3 / MET receptor recycling / MET activates RAP1 and RAC1 / MET interacts with TNS proteins / MET activates PTK2 signaling / MET activates PTPN11 / MET activates PI3K/AKT signaling / MET activates RAS signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / MET Receptor Activation / Interleukin-4 and Interleukin-13 signaling / Negative regulation of MET activity / PIP3 activates AKT signaling / Interleukin-7 signaling / PAN/Apple domain profile. / Constitutive Signaling by Aberrant PI3K in Cancer / Platelet degranulation / positive regulation of neuron projection regeneration / regulation of tau-protein kinase activity / regulation of p38MAPK cascade / myoblast proliferation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / negative regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of myelination / positive regulation of interleukin-10 production / hepatocyte growth factor receptor signaling pathway / hyaluronan metabolic process / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / epithelial to mesenchymal transition / negative regulation of release of cytochrome c from mitochondria / negative regulation of interleukin-6 production / positive regulation of osteoblast differentiation / chemoattractant activity / negative regulation of peptidyl-serine phosphorylation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cell chemotaxis / negative regulation of autophagy / negative regulation of inflammatory response / platelet alpha granule lumen / liver development / cell morphogenesis / animal organ regeneration / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / growth factor activity / positive regulation of angiogenesis / Ras guanyl-nucleotide exchange factor activity / platelet degranulation / positive regulation of peptidyl-tyrosine phosphorylation / phosphatidylinositol-4,5-bisphosphate 3-kinase activity / mitotic cell cycle / positive regulation of phosphatidylinositol 3-kinase signaling / activation of MAPK activity / MAPK cascade / protein tyrosine kinase activity / positive regulation of cell migration / positive regulation of protein phosphorylation / positive regulation of protein kinase B signaling / cytokine-mediated signaling pathway / serine-type endopeptidase activity / protein heterodimerization activity / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / membrane / extracellular region / identical protein binding / Hepatocyte growth factor / Uncharacterized protein
Function and homology information
Specimen sourceHOMO 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 21, 2014 / Release: Jan 13, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 13, 2016Structure modelrepositoryInitial release
1.1Aug 29, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.title

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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
Polyers68,4483
Non-polymers00
Water39622
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4980
ΔGint (kcal/M)-29.6
Surface area (Å2)26130
MethodPISA
Unit cell
γ
α
β
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-MC 2 2 21

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Components

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


Mass: 22242.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-210 / Mutation: YES / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14210
#2: Protein/peptide SFN68 FAB


Mass: 23230.957 Da / Num. of mol.: 1 / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Details: RABBIT/HUMAN CHIMERIC ANTIBODY
#3: Protein/peptide SFN68 FAB


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


Mass: 18.015 Da / Num. of mol.: 22 / Formula: H2O / Water

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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.
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
Rfree0.2975813475 %
Rwork0.2676--
obs0.269132554195.51 %
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. atoms422500224247
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0120.024329
r_bond_other_d0.0070.023967
r_angle_refined_deg1.4561.955882
r_angle_other_deg0.8353.0049161
r_dihedral_angle_1_deg6.155549
r_dihedral_angle_2_deg34.4924.36172
r_dihedral_angle_3_deg15.56315691
r_dihedral_angle_4_deg15.6111517
r_chiral_restr0.0730.2655
r_gen_planes_refined0.0050.0214910
r_gen_planes_other0.0020.02977
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS shellResolution: 2.618→2.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42692-
Rwork0.3961586-
obs--82.58 %

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