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- PDB-6jyp: Crystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-... -

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Basic information

Entry
Database: PDB / ID: 6jyp
TitleCrystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE / Urokinase / Amiloride
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 / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex ...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 / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex / regulation of smooth muscle cell migration / 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
Chem-HMX / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBuckley, B. / Jiang, L.G. / Huang, M.D. / Kelso, M. / Ranson, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1100432 Australia
CitationJournal: To Be Published
Title: uPA-HMA
Authors: Buckley, B. / Jiang, L.G. / Huang, M.D. / Kelso, M. / Ranson, M.
History
DepositionApr 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: 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 9, 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

Downloads & links

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Assembly

Deposited unit
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1483
Polymers27,7411
Non-polymers4082
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-20 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.242, 121.242, 42.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Urokinase-type plasminogen activator / uPA


Mass: 27740.627 Da / Num. of mol.: 1 / Mutation: H99Y,C122A,N145Q
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-HMX / 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide / HMA


Mass: 311.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18ClN7O / Feature type: SUBJECT OF INVESTIGATION
#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.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.05M sodium citrate at pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→60 Å / Num. obs: 10984 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 30
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.691 / Num. unique obs: 559

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVA

4dva


Resolution: 2.25→30.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.512 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.255 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 526 4.8 %RANDOM
Rwork0.193 ---
obs0.196 10455 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.16 Å2 / Biso mean: 50.97 Å2 / Biso min: 26.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.34 Å20 Å2
2---0.34 Å20 Å2
3---1.1 Å2
Refinement stepCycle: final / Resolution: 2.25→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 26 50 2020
Biso mean--68.01 47.28 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192004
X-RAY DIFFRACTIONr_bond_other_d0.0040.021882
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9592683
X-RAY DIFFRACTIONr_angle_other_deg0.7473.0054312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0555225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69923.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8181513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212123
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 42 -
Rwork0.277 774 -
all-816 -
obs--98.79 %

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