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- PDB-5wxp: Crystal structure of uPA in complex with upain-2-3-W3A -

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Basic information

Entry
Database: PDB / ID: 5wxp
TitleCrystal structure of uPA in complex with upain-2-3-W3A
Components
  • Urokinase-type plasminogen activator chain B
  • upain-2-3-W3A peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine proteases / uPA / pepetide inhibitors / HYDROLASE-HYDROLASE INHIBITOR 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 / 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. / 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
ALANINE / CYSTEINE / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
Phage display vector pTDisp (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsJiang, L. / Huang, M.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Cleavage of peptidic inhibitors by target protease is caused by peptide conformational transition.
Authors: Jiang, L. / Oldenburg, E. / Kromann-Hansen, T. / Xu, P. / Jensen, J.K. / Andreasen, P.A. / Huang, M.
History
DepositionJan 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: Urokinase-type plasminogen activator chain B
P: upain-2-3-W3A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1364
Polymers28,9262
Non-polymers2102
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-1 kcal/mol
Surface area11470 Å2
Unit cell
Length a, b, c (Å)120.821, 120.821, 42.278
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 Urokinase-type plasminogen activator chain B / uPA


Mass: 28442.373 Da / Num. of mol.: 1 / Mutation: C299A/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
#2: Protein/peptide upain-2-3-W3A peptide


Mass: 483.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phage display vector pTDisp (others)
#3: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCOMPLETE SEQUENCE OF UPAIN-2-3W3A PEPTIDE IS CSA(7XC)GLENHAAC. THIS PEPTIDE WAS HYDROLYZED BY ...COMPLETE SEQUENCE OF UPAIN-2-3W3A PEPTIDE IS CSA(7XC)GLENHAAC. THIS PEPTIDE WAS HYDROLYZED BY SERINE PROTEASE (UPA), ONLY N-TERMINAL RESIDUES CSA(7XC) AND C-TERMINAL RESIDUES AC WERE OBSERVED. MEANWHILE, N-TERMINAL CYS AND C-TERMINAL CYS LINKED TOGETHER THROUGH SSBOND.

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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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 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 315r / Detector: CCD / Date: Nov 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→60 Å / Num. obs: 22375 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 36.4
Reflection shellRmerge(I) obs: 0.788

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementStarting model: 4DVA

4dva


Resolution: 1.75→39.23 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.44 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1146 5.1 %RANDOM
Rwork0.213 ---
obs0.215 21226 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.21 Å20 Å2
2---0.21 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 12 69 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192033
X-RAY DIFFRACTIONr_bond_other_d0.0020.021915
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9522717
X-RAY DIFFRACTIONr_angle_other_deg0.733.0054382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42423.29588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3641513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
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: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 79 -
Rwork0.308 1557 -
obs--95.56 %

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