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- PDB-5lhp: The p-aminobenzamidine active site inhibited catalytic domain of ... -

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Basic information

Entry
Database: PDB / ID: 5lhp
TitleThe p-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7
Components
  • Camelid-Derived Antibody Fragment
  • Urokinase-type plasminogen activator
KeywordsHYDROLASE / Trypsin-like serine proteases / Nanobody / Inhibitor
Function / homology
Function and homology information


Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / skeletal muscle tissue regeneration / negative regulation of plasminogen activation ...Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / skeletal muscle tissue regeneration / negative regulation of plasminogen activation / serine-type endopeptidase complex / smooth muscle cell migration / plasminogen activation / positive regulation of smooth muscle cell migration / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / Neutrophil degranulation / positive regulation of reactive oxygen species metabolic process / peptidase activity / regulation of cell population proliferation / angiogenesis / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / extracellular space
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. ...Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, serine 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
P-AMINO BENZAMIDINE / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsKromann-Hansen, T. / Lange, E.L. / Sorensen, H.P. / Ghassabeh, G.H. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Andreasen, P.A.
Funding support Denmark, China, 4items
OrganizationGrant numberCountry
Danish National Research Foundation26-331-6 Denmark
Natural Science Foundation of China31161130356, 31170707, 31370737 China
Lundbeck FoundationR83-A7826 Denmark
Carlsberg FoundationCF15-0814 Denmark
CitationJournal: Sci Rep / Year: 2017
Title: Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator.
Authors: Kromann-Hansen, T. / Louise Lange, E. / Peter Srensen, H. / Hassanzadeh-Ghassabeh, G. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Komives, E.A. / Andreasen, P.A.
History
DepositionJul 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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: Urokinase-type plasminogen activator
B: Camelid-Derived Antibody Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,46319
Polymers43,8582
Non-polymers1,60517
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-144 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.080, 94.080, 122.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Urokinase-type plasminogen activator / uPA


Mass: 27554.158 Da / Num. of mol.: 1 / Mutation: C122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plau / Production host: Escherichia coli (E. coli) / References: UniProt: P06869, u-plasminogen activator
#2: Antibody Camelid-Derived Antibody Fragment


Mass: 16303.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 101 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 100 mM HEPES, 1.6 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.63→40.738 Å / Num. obs: 18943 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 22.94
Reflection shellResolution: 2.63→2.77 Å / Rmerge(I) obs: 1.017

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHR, 4JVP

5lhr

4jvp


Resolution: 2.63→40.738 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 947 5 %
Rwork0.2061 --
obs0.2072 18942 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→40.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 87 84 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113079
X-RAY DIFFRACTIONf_angle_d1.4594174
X-RAY DIFFRACTIONf_dihedral_angle_d14.7141094
X-RAY DIFFRACTIONf_chiral_restr0.065423
X-RAY DIFFRACTIONf_plane_restr0.008534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.76870.4111340.35592557X-RAY DIFFRACTION100
2.7687-2.94210.32221340.28972537X-RAY DIFFRACTION100
2.9421-3.16910.27851330.25532532X-RAY DIFFRACTION100
3.1691-3.48790.22471350.21512568X-RAY DIFFRACTION100
3.4879-3.99230.24361350.18922549X-RAY DIFFRACTION99
3.9923-5.02830.15991360.15752593X-RAY DIFFRACTION99
5.0283-40.74270.21331400.19632659X-RAY DIFFRACTION97

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