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- PDB-4x1s: The crystal structure of mupain-1-16-D9A in complex with murinise... -

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Basic information

Entry
Database: PDB / ID: 4x1s
TitleThe crystal structure of mupain-1-16-D9A 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 / 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
piperidine-1-carboximidamide / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, L. / Zhao, B. / Xu, P. / Andreasen, P. / Huang, M.
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 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-1-16
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0583
Polymers28,9312
Non-polymers1271
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-6 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.300, 121.300, 42.926
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: 1061.232 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: catalytic domain (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
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: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.897→60 Å / Num. obs: 18056 / % possible obs: 97 % / Redundancy: 3.4 % / Net I/σ(I): 32.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWN

2nwn


Resolution: 1.9→24.11 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 925 5.12 %
Rwork0.205 --
obs0.208 18052 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 9 67 2092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082081
X-RAY DIFFRACTIONf_angle_d1.1112809
X-RAY DIFFRACTIONf_dihedral_angle_d14.783760
X-RAY DIFFRACTIONf_chiral_restr0.047303
X-RAY DIFFRACTIONf_plane_restr0.006355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8967-1.99660.28241340.26232410X-RAY DIFFRACTION96
1.9966-2.12160.3021330.23952479X-RAY DIFFRACTION98
2.1216-2.28530.27671190.22932485X-RAY DIFFRACTION98
2.2853-2.51510.31021400.22462496X-RAY DIFFRACTION98
2.5151-2.87850.27091350.22272490X-RAY DIFFRACTION99
2.8785-3.62470.2221410.22493X-RAY DIFFRACTION99
3.6247-24.10890.2271230.18062274X-RAY DIFFRACTION90

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