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- PDB-4mnx: Crystal structure of urokinase-type plasminogen activator (uPA) c... -

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Basic information

Entry
Database: PDB / ID: 4mnx
TitleCrystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK811
Components
  • Urokinase-type plasminogen activator chain B
  • bicyclic peptide UK811
KeywordsHYDROLASE/HYDROLASE INHIBITOR / competitive inhibitor / bicyclic peptide / inhibitor / protease / 1 / 1' / 1''-(1 / 3 / 5-triazinane-1 / 5-triyl)triprop-2-en-1-one (TATA) cyclization / extracellular / 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
bicyclic peptide UK811 / Chem-29N / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, S. / Pojer, F. / Heinis, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Peptide ligands stabilized by small molecules.
Authors: Chen, S. / Bertoldo, D. / Angelini, A. / Pojer, F. / Heinis, C.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator chain B
B: bicyclic peptide UK811
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6976
Polymers29,1572
Non-polymers5404
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-28 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.450, 53.500, 79.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Urokinase-type plasminogen activator chain B / U-plasminogen activator / uPA


Mass: 27586.420 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 179-423) / Mutation: C122A, N145Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pSecTagA / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P00749, u-plasminogen activator
#2: Protein/peptide bicyclic peptide UK811


Type: Cyclic peptide / Class: Inhibitor / Mass: 1570.820 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: modified with 1,3,5-triacryloyl-1,3,5-triazinane (TATA)
References: bicyclic peptide UK811

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Non-polymers , 4 types, 132 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-29N / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form


Type: Cyclic peptide / Class: Inhibitor / Mass: 255.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O3 / References: bicyclic peptide UK811
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG4000, 15% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2013
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→44.4 Å / Num. all: 19688 / Num. obs: 19325 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2 / Num. unique all: 2762 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→43.83 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.822 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22657 990 5.1 %RANDOM
Rwork0.18903 ---
all0.19091 19688 --
obs0.19091 18289 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.686 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---2.16 Å2-0 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 34 128 2203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192130
X-RAY DIFFRACTIONr_bond_other_d0.0020.021977
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9612888
X-RAY DIFFRACTIONr_angle_other_deg0.7773.0064542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92923.11893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3781515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 77 -
Rwork0.292 1298 -
obs--96.02 %

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