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- PDB-3k2u: Crystal structure of HGFA in complex with the allosteric inhibito... -

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Basic information

Entry
Database: PDB / ID: 3k2u
TitleCrystal structure of HGFA in complex with the allosteric inhibitory antibody Fab40
Components
  • (Antibody, Fab fragment, ...) x 2
  • (Hepatocyte growth factor activator ...) x 2
KeywordsHYDROLASE/IMMUNE SYSTEM / Serine Protease / Allosteric inhibitor / Antibody / EGF-like domain / GLYCOPROTEIN / Fab complex / HYDROLASE / Disulfide bond / Kringle / Protease / Secreted / Zymogen / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor activator serine protease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGanesan, R. / Eigenbrot, C. / Shia, S.
CitationJournal: Structure / Year: 2009
Title: Unraveling the allosteric mechanism of serine protease inhibition by an antibody.
Authors: Ganesan, R. / Eigenbrot, C. / Wu, Y. / Liang, W.C. / Shia, S. / Lipari, M.T. / Kirchhofer, D.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 27, 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 activator long chain
B: Hepatocyte growth factor activator short chain
H: Antibody, Fab fragment, Heavy Chain
L: Antibody, Fab fragment, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3795
Polymers78,9554
Non-polymers4241
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-27 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.944, 48.933, 96.034
Angle α, β, γ (deg.)98.10, 95.01, 103.89
Int Tables number1
Space group name H-MP1

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Components

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Hepatocyte growth factor activator ... , 2 types, 2 molecules AB

#1: Protein Hepatocyte growth factor activator long chain / HGF activator / HGFA


Mass: 27982.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia Ni (cabbage looper)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Hepatocyte growth factor activator short chain / HGF activator / HGFA


Mass: 3962.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia Ni (cabbage looper)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Antibody , 2 types, 2 molecules HL

#3: Antibody Antibody, Fab fragment, Heavy Chain


Mass: 23770.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3
#4: Antibody Antibody, Fab fragment, Light Chain


Mass: 23238.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3

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Sugars / Non-polymers , 2 types, 169 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% PEG 10,000, 100 mM HEPES pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 61952 / Num. obs: 30979 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 37.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.198

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R0L

2r0l


Resolution: 2.35→19.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 894977.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2653 9.9 %RANDOM
Rwork0.239 ---
obs0.239 26714 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9654 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 66.6 Å2
Baniso -1Baniso -2Baniso -3
1-27.76 Å212.16 Å213.89 Å2
2---20.69 Å28.1 Å2
3----7.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5011 0 28 168 5207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.15
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.423 392 9.6 %
Rwork0.392 3706 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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