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- PDB-5yc7: The crystal structure of uPA in complex with 4-Bromobenzylamirne ... -

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Basic information

Entry
Database: PDB / ID: 5yc7
TitleThe crystal structure of uPA in complex with 4-Bromobenzylamirne at pH7.4
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE/HYDROLASE INHIBITOR / halogen bonding / serine protease / uPA / P1 group / protease 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 signaling receptor activity / regulation of smooth muscle cell migration ...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 signaling receptor activity / regulation of smooth muscle cell migration / 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. ...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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
1-(4-BROMOPHENYL)METHANAMINE / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJiang, L.G. / Zhang, X. / Huang, M.D.
CitationJournal: Rsc Adv / Year: 2018
Title: Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases
Authors: Jiang, L.G. / Zhang, X. / Zhou, Y. / Chen, Y.Y. / Luo, Z.P. / Li, J.Y. / Yuan, C. / Huang, M.D.
History
DepositionSep 6, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 3, 2018ID: 4JNL
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9983
Polymers27,7161
Non-polymers2822
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-22 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.575, 121.575, 42.212
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 / uPA


Mass: 27715.600 Da / Num. of mol.: 1
Fragment: Urokinase-type plasminogen activator chain B, UNP residues 179-324
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: Chemical ChemComp-PZH / 1-(4-BROMOPHENYL)METHANAMINE / 4-BROMOBENZYLAMINE


Mass: 186.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8BrN
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50mM sodium citrate (pH 4.6), 2.0M ammonium sulfate supplemented with 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 15624 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.6
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVA

4dva


Resolution: 2→60.79 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.667 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26158 777 5 %RANDOM
Rwork0.21192 ---
obs0.21431 14847 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å2-0 Å2
2--0.27 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2→60.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 14 39 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191989
X-RAY DIFFRACTIONr_bond_other_d0.0020.021864
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9492661
X-RAY DIFFRACTIONr_angle_other_deg0.88934283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32723.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5681513
X-RAY DIFFRACTIONr_chiral_restr0.080.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
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_it2.9055.264963
X-RAY DIFFRACTIONr_mcbond_other2.8955.258962
X-RAY DIFFRACTIONr_mcangle_it4.4817.7381167
X-RAY DIFFRACTIONr_mcangle_other4.487.7441168
X-RAY DIFFRACTIONr_scbond_it3.5135.8961026
X-RAY DIFFRACTIONr_scbond_other3.4985.8841023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4598.6221489
X-RAY DIFFRACTIONr_long_range_B_refined9.28143.7242194
X-RAY DIFFRACTIONr_long_range_B_other9.2543.7012190
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 50 -
Rwork0.277 1068 -
obs--97.05 %

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