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- PDB-2wub: Crystal structure of HGFA in complex with the allosteric non- inh... -

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Basic information

Entry
Database: PDB / ID: 2wub
TitleCrystal structure of HGFA in complex with the allosteric non- inhibitory antibody Fab40.deltaTrp
Components
  • (FAB FRAGMENT FAB40.DELTATRP ...) x 2
  • (HEPATOCYTE GROWTH FACTOR ACTIVATOR ...) x 2
KeywordsHYDROLASE/IMMUNE SYSTEM / HYDROLASE IMMUNE SYSTEM COMPLEX / DISULFIDE BOND / SERINE PROTEASE / EGF-LIKE DOMAIN / ALLOSTERIC INHIBITOR / KRINGLE / ZYMOGEN / PROTEASE / SECRETED / ANTIBODY / HYDROLASE / FAB COMPLEX / POLYMORPHISM / GLYCOPROTEIN / 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 / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor activator
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionOct 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
C: HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN
D: HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN
H: FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN
L: FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
Q: FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
R: FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,71010
Polymers157,5378
Non-polymers1,1732
Water2,774154
1
C: HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN
D: HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN
Q: FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
R: FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3555
Polymers78,7684
Non-polymers5871
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-27 kcal/mol
Surface area28350 Å2
MethodPISA
2
A: HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN
B: HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN
H: FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN
L: FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3555
Polymers78,7684
Non-polymers5871
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-28.8 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.356, 89.530, 118.470
Angle α, β, γ (deg.)90.00, 91.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HEPATOCYTE GROWTH FACTOR ACTIVATOR ... , 2 types, 4 molecules ACBD

#1: Protein HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN


Mass: 27982.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-GLYCOSYLATION AT ASN74 / 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


Mass: 3962.654 Da / Num. of mol.: 2
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, 4 molecules HRLQ

#3: Antibody FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN


Mass: 23584.395 Da / Num. of mol.: 2
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 FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN


Mass: 23238.748 Da / Num. of mol.: 2
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, 156 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 53.85 % / Description: NONE
Crystal growpH: 7.5 / Details: 10% PEG 10,000, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 33747 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 113.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R0L

2r0l


Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1089100.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3318 10 %RANDOM
Rwork0.216 ---
obs0.216 33230 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.5973 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 70.9 Å2
Baniso -1Baniso -2Baniso -3
1-13.65 Å20 Å2-1.55 Å2
2---6.71 Å20 Å2
3----6.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9966 0 78 154 10198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 558 10.3 %
Rwork0.313 4880 -
obs--98.3 %
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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