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- PDB-3oy6: The crystal structure of uPA complex with peptide inhibitor MH036... -

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Basic information

Entry
Database: PDB / ID: 3oy6
TitleThe crystal structure of uPA complex with peptide inhibitor MH036 at pH4.6
Components
  • MH036
  • Urokinase-type plasminogen activator
KeywordsHYDROLASE/HYDROLASE INHIBITOR / UROKINASE-TYPE PLASMINOGEN ACTIVATOR / PEPTIDYL INHIBITOR / PHARMACOPHORE / HYDROLASE / 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 / 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
Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsJiang, L.G. / Andreasen, P.A. / Huang, M.D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The binding mechanism of a peptidic cyclic serine protease inhibitor
Authors: Jiang, L.G. / Svane, A.S.P. / Sorensen, H.P. / Jensen, J.K. / Hosseini, M. / Chen, Z. / Weydert, C. / Nielsen, J.T. / Christensen, A. / Yuan, C. / Jensen, K.J. / Nielsen, N.C. / Malmendal, A. ...Authors: Jiang, L.G. / Svane, A.S.P. / Sorensen, H.P. / Jensen, J.K. / Hosseini, M. / Chen, Z. / Weydert, C. / Nielsen, J.T. / Christensen, A. / Yuan, C. / Jensen, K.J. / Nielsen, N.C. / Malmendal, A. / Huang, M.D. / Andreasen, P.A.
History
DepositionSep 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq_dif.details
Revision 1.3Oct 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
P: MH036


Theoretical massNumber of molelcules
Total (without water)30,7832
Polymers30,7832
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-2 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.091, 121.091, 43.332
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 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: 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): X33 / References: UniProt: P00749, u-plasminogen activator
#2: Protein/peptide MH036


Mass: 2340.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.05M SODIUM CITRATE, 1.95M (NH4)2SO4, 0.05% NAN3, 5% PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→60 Å / Num. all: 10379 / Num. obs: 10358 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Rsym value: 0.043 / Net I/σ(I): 52.7
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 41.5 / Num. unique all: 515 / Rsym value: 0.054 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NWN

2nwn


Resolution: 2.31→40.05 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.862 / SU B: 7.317 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26262 498 4.8 %RANDOM
Rwork0.18141 ---
obs0.18526 9877 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.639 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.31→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 0 125 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212125
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9412877
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6823.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72715361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6291515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211604
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5771.51296
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10222091
X-RAY DIFFRACTIONr_scbond_it1.3743829
X-RAY DIFFRACTIONr_scangle_it2.3814.5786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.311→2.371 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 44 -
Rwork0.17 753 -
obs--100 %

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