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- PDB-5lsp: 107_A07 Fab in complex with fragment of the Met receptor -

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Basic information

Entry
Database: PDB / ID: 5lsp
Title107_A07 Fab in complex with fragment of the Met receptor
Components
  • (Hepatocyte growth factor ...) x 2
  • 107_A07 Fab heavy chain
  • 107_A07 Fab light chain
KeywordsTRANSFERASE / Fab / beta propeller / Ig-like domain / cell signalling / Met receptor / antibody binding
Function / homology
Function and homology information


negative regulation of guanyl-nucleotide exchange factor activity / 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 / endothelial cell morphogenesis / semaphorin receptor activity / MET receptor recycling / pancreas development ...negative regulation of guanyl-nucleotide exchange factor activity / 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 / endothelial cell morphogenesis / semaphorin receptor activity / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of Rho protein signal transduction / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / establishment of skin barrier / MET activates RAS signaling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / cell surface receptor protein tyrosine kinase signaling pathway / liver development / molecular function activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / basal plasma membrane / excitatory postsynaptic potential / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / Negative regulation of MET activity / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / protein phosphatase binding / receptor complex / cell surface receptor signaling pathway / postsynapse / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsDiCara, D. / Chirgadze, D.Y. / Pope, A. / Karatt-Vellatt, A. / Winter, A. / van den Heuvel, J. / Gherardi, E. / McCafferty, J.
CitationJournal: Sci Rep / Year: 2017
Title: Characterization and structural determination of a new anti-MET function-blocking antibody with binding epitope distinct from the ligand binding domain.
Authors: DiCara, D.M. / Chirgadze, D.Y. / Pope, A.R. / Karatt-Vellatt, A. / Winter, A. / Slavny, P. / van den Heuvel, J. / Parthiban, K. / Holland, J. / Packman, L.C. / Mavria, G. / Hoffmann, J. / ...Authors: DiCara, D.M. / Chirgadze, D.Y. / Pope, A.R. / Karatt-Vellatt, A. / Winter, A. / Slavny, P. / van den Heuvel, J. / Parthiban, K. / Holland, J. / Packman, L.C. / Mavria, G. / Hoffmann, J. / Birchmeier, W. / Gherardi, E. / McCafferty, J.
History
DepositionSep 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatocyte growth factor receptor
H: 107_A07 Fab heavy chain
L: 107_A07 Fab light chain
P: Hepatocyte growth factor receptor
S: 107_A07 Fab heavy chain
T: 107_A07 Fab light chain
X: Hepatocyte growth factor receptor
Y: Hepatocyte growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,67610
Polymers149,2348
Non-polymers4422
Water1,58588
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-59 kcal/mol
Surface area57320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 82.279, 267.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Hepatocyte growth factor ... , 2 types, 4 molecules APXY

#1: Protein Hepatocyte growth factor receptor / HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / ...HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / Tyrosine-protein kinase Met


Mass: 25592.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Plasmid: pA71d / Cell line (production host): Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P08581, receptor protein-tyrosine kinase
#4: Protein/peptide Hepatocyte growth factor receptor / HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / ...HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / Tyrosine-protein kinase Met


Mass: 1627.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Plasmid: pA71d / Cell line (production host): Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P08581, receptor protein-tyrosine kinase

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Antibody , 2 types, 4 molecules HSLT

#2: Antibody 107_A07 Fab heavy chain


Mass: 23891.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody 107_A07 Fab light chain


Mass: 23504.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars / Non-polymers , 2 types, 90 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 20,000, 20% PEG 550-MME, 0.1M Trizma/Bicine pH 8.5, 0.03M magnesium chloride, 0.03M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91376 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91376 Å / Relative weight: 1
ReflectionResolution: 2.6→48.95 Å / Num. obs: 49099 / % possible obs: 99 % / Redundancy: 5.5 % / Biso Wilson estimate: 50.2 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.745.50.8832195.8
8.23-48.954.90.03233.6199

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.605→48.942 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 27.53
RfactorNum. reflection% reflection
Rfree0.2565 2000 4.09 %
Rwork0.2154 --
obs0.2171 48940 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.605→48.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10043 0 28 88 10159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510319
X-RAY DIFFRACTIONf_angle_d0.99914001
X-RAY DIFFRACTIONf_dihedral_angle_d13.6013691
X-RAY DIFFRACTIONf_chiral_restr0.041593
X-RAY DIFFRACTIONf_plane_restr0.0051785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6051-2.67020.39321330.34223101X-RAY DIFFRACTION92
2.6702-2.74240.36731400.31343311X-RAY DIFFRACTION99
2.7424-2.82310.32161400.2993282X-RAY DIFFRACTION99
2.8231-2.91420.32971410.28563310X-RAY DIFFRACTION99
2.9142-3.01840.30621420.27663324X-RAY DIFFRACTION99
3.0184-3.13920.32181430.26833344X-RAY DIFFRACTION99
3.1392-3.2820.30551410.25223327X-RAY DIFFRACTION99
3.282-3.4550.25621430.23333345X-RAY DIFFRACTION99
3.455-3.67140.29751420.22033356X-RAY DIFFRACTION100
3.6714-3.95480.24411440.20853373X-RAY DIFFRACTION100
3.9548-4.35260.23221450.18273385X-RAY DIFFRACTION99
4.3526-4.98190.20271440.16133398X-RAY DIFFRACTION100
4.9819-6.27460.22871480.18393462X-RAY DIFFRACTION100
6.2746-48.9510.20241540.18343622X-RAY DIFFRACTION99

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