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- PDB-3khv: Crystal Structures of Urokinase-type Plasminogen Activator in Com... -

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Basic information

Entry
Database: PDB / ID: 3khv
TitleCrystal Structures of Urokinase-type Plasminogen Activator in Complex with 4-(Aminomethyl) Benzoic Acid and 4-(Aminomethyl-phenyl)-methanol
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE / PROTEIN-LIGAND COMPLEX / Disulfide bond / Fibrinolysis / Plasminogen activation / Serine protease
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. ...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 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
[4-(aminomethyl)phenyl]methanol / TRIETHYLENE GLYCOL / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJiang, L.-G. / Zhao, G.-X. / Bian, X.-B. / Yuan, C. / Huang, Z.-X. / Huang, M.-D.
CitationJournal: CHIN.J.STRUCT.CHEM. / Year: 2009
Title: Crystal Structures of Urokinase-type Plasminogen Activator in Complex with 4-(Aminomethyl) Benzoic Acid and 4-(Aminomethyl-phenyl)-methanol
Authors: Jiang, L.-G. / Zhao, G.-X. / Bian, X.-B. / Yuan, C. / Huang, Z.-X. / Huang, M.-D.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8264
Polymers28,4421
Non-polymers3833
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.826, 120.826, 42.355
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 / U-plasminogen activator / uPA / Urokinase-type plasminogen activator chain B


Mass: 28442.373 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 179-431 / Mutation: C122A, N145Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P00749, u-plasminogen activator
#2: Chemical ChemComp-4AL / [4-(aminomethyl)phenyl]methanol


Mass: 137.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE WATER MOLECULE S205 DESCRIBED IN THE ASSOCIATED ARTICLE IS CALLED AS A 449 IN THIS ENTRY.
Sequence detailsTHE PDB IS NUMBERED BY CHYMOTRYPSINOGEN NUMBERING OF SERINE PROTEINASES AND THUS INCLUDES INSERTION CODES.

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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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.05M sodium citrate, 1.95M (NH4)2SO4, 0.05% NaN3, 5% PEG 400, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→39.26 Å / Num. all: 9681 / Num. obs: 9307 / % possible obs: 96.14 % / Redundancy: 4.24 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.0951 / Net I/σ(I): 6.22
Reflection shellResolution: 2.35→2.5 Å / Redundancy: 4.56 % / Mean I/σ(I) obs: 6.61 / Num. unique all: 8043 / Rsym value: 0.392 / % possible all: 99.19

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Processing

Software
NameVersionClassification
CNS1.1refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NWN

2nwn


Resolution: 2.35→39.26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1769943.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.293 968 10.5 %RANDOM
Rwork0.228 ---
obs0.228 9238 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 96.8751 Å2 / ksol: 0.390941 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å20.74 Å20 Å2
2---3.57 Å20 Å2
3---7.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 25 260 2175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 107 8.2 %
Rwork0.286 1203 -
obs--82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2AMP_par.txt
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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