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- PDB-4x1n: The crystal structure of mupain-1-16 in complex with murinised hu... -

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Basic information

Entry
Database: PDB / ID: 4x1n
TitleThe crystal structure of mupain-1-16 in complex with murinised human uPA at pH7.4
Components
  • Urokinase-type plasminogen activator
  • mupain-1-16
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Serine protease / peptidic inhibitor / uPA / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex / regulation of smooth muscle cell migration / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
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, 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 / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
piperidine-1-carboximidamide / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJiang, L. / Zhao, B. / Xu, P. / Andreasen, P. / Huang, M.
Funding support China, Denmark, 6items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31161130356 China
the National Natural Science Foundation of China30770429 China
the Natural Science Foundation of Fujian Province2012J05071 China
the Lundbeck FoundationR83-A7826 Denmark
The Carlsberg Foundation2012_01_0642 Denmark
Aarhus University Research FoundationReference Number 10 Denmark
CitationJournal: Plos One / Year: 2014
Title: A cyclic peptidic serine protease inhibitor: increasing affinity by increasing peptide flexibility.
Authors: Zhao, B. / Xu, P. / Jiang, L. / Paaske, B. / Kromann-Hansen, T. / Jensen, J.K. / Srensen, H.P. / Liu, Z. / Nielsen, J.T. / Christensen, A. / Hosseini, M. / Srensen, K.K. / Nielsen, N.C. / ...Authors: Zhao, B. / Xu, P. / Jiang, L. / Paaske, B. / Kromann-Hansen, T. / Jensen, J.K. / Srensen, H.P. / Liu, Z. / Nielsen, J.T. / Christensen, A. / Hosseini, M. / Srensen, K.K. / Nielsen, N.C. / Jensen, K.J. / Huang, M. / Andreasen, P.A.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Experimental preparation
Revision 1.2Nov 8, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: mupain-1-16
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1023
Polymers28,9752
Non-polymers1271
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.595, 121.595, 42.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide mupain-1-16


Mass: 1105.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Urokinase-type plasminogen activator / uPA


Mass: 27869.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 179-425 / Mutation: C299A, H272Y, N322Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Komagataella pastoris (fungus) / References: UniProt: P00749, u-plasminogen activator
#3: Chemical ChemComp-MRZ / piperidine-1-carboximidamide


Mass: 127.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0M ammonium sulfate, 50mM sodium citrate pH 4.6, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21312 / % possible obs: 98.7 %

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWN

2nwn


Resolution: 1.8→35.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.402 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27619 1089 5.1 %RANDOM
Rwork0.22971 ---
obs0.23214 20223 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.92 Å20 Å2
2---0.92 Å2-0 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 9 65 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192073
X-RAY DIFFRACTIONr_bond_other_d0.0010.021953
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9542774
X-RAY DIFFRACTIONr_angle_other_deg0.7333.0054478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09323.29791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1715349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0611513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 76 -
Rwork0.327 1504 -
obs--97.11 %

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