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- PDB-4x0w: The crystal structure of mupain-1-17 in complex with murinised hu... -

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Basic information

Entry
Database: PDB / ID: 4x0w
TitleThe crystal structure of mupain-1-17 in complex with murinised human uPA
Components
  • Urokinase-type plasminogen activatorUrokinase
  • mupain-1-17
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Serine protease / peptidic inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex / 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 / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...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 / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / 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. / EGF-like domain signature 1. ...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 / 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 / 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 / Resolution: 2.1 Å
AuthorsJiang, L. / Zhao, B. / Xu, P. / Andreasen, P. / Huang, M.
Funding support China, Denmark, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31161130356 China
National Natural Science Foundation of China31170707 China
Fujian Province2012J05071 China
the Danish National Research Foundation26-331-6 Denmark
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2015
Title: Distinctive binding modes and inhibitory mechanisms of two peptidic inhibitors of urokinase-type plasminogen activator with isomeric P1 residues.
Authors: Jiang, L. / Zhao, B. / Xu, P. / Srensen, H.P. / Jensen, J.K. / Christensen, A. / Hosseini, M. / Nielsen, N.C. / Jensen, K.J. / Andreasen, P.A. / Huang, M.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: mupain-1-17
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1984
Polymers28,9752
Non-polymers2232
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-22 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.641, 120.641, 42.657
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-1-17


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


Mass: 27869.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 179-425 / Mutation: H99Y, C122A, N145Q
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 40.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0 M ammonium sulfate, 50 mM 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: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 12802 / % possible obs: 94.6 % / Redundancy: 2 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
Cootmodel building
RefinementResolution: 2.1→60.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27222 639 5 %RANDOM
Rwork0.23603 ---
obs0.23788 12159 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.523 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0.88 Å20 Å2
2---1.76 Å20 Å2
3---2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 14 29 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0480.0222096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8071.9592840
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6085252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02623.29791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05115349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3651513
X-RAY DIFFRACTIONr_chiral_restr0.1430.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211568
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1981.51268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0722048
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9473828
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2854.5792
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 48 -
Rwork0.281 941 -
obs--96.96 %

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