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- PDB-4gly: Human urokinase-type plasminogen activator uPA in complex with th... -

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Basic information

Entry
Database: PDB / ID: 4gly
TitleHuman urokinase-type plasminogen activator uPA in complex with the two-disulfide bridge peptide UK504
Components
  • BICYCLIC PEPTIDE INHIBITOR UK504
  • Urokinase-type plasminogen activator
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease / chymotrypsin fold / urokinase-type plasminogen activator / bicyclic peptide inhibitor / 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 INHIBITOR UK504 / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.518 Å
AuthorsButh, S.A. / Leiman, P.G. / Chen, S. / Heinis, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Bicyclic Peptide Ligands Pulled out of Cysteine-Rich Peptide Libraries.
Authors: Chen, S. / Rentero Rebollo, I. / Buth, S.A. / Morales-Sanfrutos, J. / Touati, J. / Leiman, P.G. / Heinis, C.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_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 INHIBITOR UK504
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,96213
Polymers29,0512
Non-polymers91111
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint1 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.800, 120.800, 43.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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

#1: Protein Urokinase-type plasminogen activator / 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, UROKINASE-TYPE PLASMINOGEN ACTIVATOR
Mutation: C122A, N145Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 9606 / 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 INHIBITOR UK504


Type: Cyclic peptide / Class: Inhibitor / Mass: 1464.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic (others) / References: BICYCLIC PEPTIDE INHIBITOR UK504

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Non-polymers , 6 types, 321 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsBICYCLIC PEPTIDE INHIBITOR UK504

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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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8M Ammonium sulfate, 5% PEG400, 0.05% Sodium azide, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2012
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry and a toroidal mirror (M2)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.518→29.13 Å / Num. all: 36222 / Num. obs: 36222 / % possible obs: 100 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.099
Reflection shellResolution: 1.518→1.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5284 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NWN

2nwn


Resolution: 1.518→29.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.923 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 6 / σ(I): 3 / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20416 1784 5 %RANDOM
Rwork0.12808 ---
obs0.1318 34197 99.33 %-
all-36227 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.622 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.08 Å20 Å2
2---0.08 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.518→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 50 310 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192150
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9632910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16622.76694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74415362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1421517
X-RAY DIFFRACTIONr_chiral_restr0.160.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211600
X-RAY DIFFRACTIONr_rigid_bond_restr5.6432150
X-RAY DIFFRACTIONr_sphericity_free52.906584
X-RAY DIFFRACTIONr_sphericity_bonded20.46152329
LS refinement shellResolution: 1.518→1.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 144 -
Rwork0.14 2528 -
obs-2528 100 %

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