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- PDB-4os6: Crystal structure of urokinase-type plasminogen activator (uPA) c... -

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Basic information

Entry
Database: PDB / ID: 4os6
TitleCrystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK604 (bicyclic 2)
Components
  • Urokinase-type plasminogen activatorUrokinase
  • bicyclic peptide UK604 (bicyclic 2)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bicyclic peptide / inhibitor / protease / disulfide bridges / 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 / 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
bicyclic peptide UK604 (bicyclic 2) / ACETATE ION / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, S. / Pojer, F. / Heinis, C.
CitationJournal: Nat Chem / Year: 2014
Title: Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides.
Authors: Chen, S. / Gopalakrishnan, R. / Schaer, T. / Marger, F. / Hovius, R. / Bertrand, D. / Pojer, F. / Heinis, C.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jun 2, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn ...entity_src_gen / struct_conn / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
B: bicyclic peptide UK604 (bicyclic 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3165
Polymers29,0652
Non-polymers2513
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-27 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.350, 53.705, 84.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Urokinase-type plasminogen activator / Urokinase / U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type ...U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type plasminogen activator short chain A / Urokinase-type plasminogen activator chain B


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): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P00749, u-plasminogen activator
#2: Protein/peptide bicyclic peptide UK604 (bicyclic 2)


Type: Cyclic peptide / Class: Inhibitor / Mass: 1478.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: bicyclic peptide UK604 (bicyclic 2)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 21% 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: DECTRIS 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: 1.75→45.35 Å / Num. all: 24699 / Num. obs: 24699 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 15.235 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.75-1.844.40.36143536199.8
5.53-45.354.40.03127.1891199.3

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Processing

Software
NameVersionClassification
PHASESphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.1 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18566 1256 5.1 %RANDOM
Rwork0.16976 ---
all0.17057 24699 --
obs0.17057 23389 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2---1.49 Å2-0 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 14 177 2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192143
X-RAY DIFFRACTIONr_bond_other_d0.0020.021993
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9542911
X-RAY DIFFRACTIONr_angle_other_deg0.7343.0054585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08422.97994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24415360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.291516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
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→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 102 -
Rwork0.22 1698 -
obs--99.89 %

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