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- PDB-5ugg: Protease Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ugg
TitleProtease Inhibitor
ComponentsPlasminogen
KeywordsHYDROLASE/INHIBITOR / Fibrinolysis / YO / Plasmin / Inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / myoblast differentiation / negative regulation of cell-substrate adhesion / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / kinase binding / Schaffer collateral - CA1 synapse / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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
Chem-89M / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLaw, R.H.P. / Wu, G. / Whisstock, J.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1029403 Australia
CitationJournal: Blood Adv / Year: 2017
Title: X-ray crystal structure of plasmin with tranexamic acid-derived active site inhibitors.
Authors: Law, R.H.P. / Wu, G. / Leung, E.W.W. / Hidaka, K. / Quek, A.J. / Caradoc-Davies, T.T. / Jeevarajah, D. / Conroy, P.J. / Kirby, N.M. / Norton, R.S. / Tsuda, Y. / Whisstock, J.C.
History
DepositionJan 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1132
Polymers27,5411
Non-polymers5731
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.550, 39.480, 62.130
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasminogen / microplasmin


Mass: 27540.615 Da / Num. of mol.: 1 / Fragment: UNP residues 562-810
Source method: isolated from a genetically manipulated source
Details: microplasmin / Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P00747, plasmin
#2: Chemical ChemComp-89M / Nalpha-[trans-4-(aminomethyl)cyclohexane-1-carbonyl]-N-octyl-O-[(quinolin-2-yl)methyl]-L-tyrosinamide


Mass: 572.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H48N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10 % (w/v) polyethylene glycol 6,000, 4 % (v/v) 2-methyl-2,4-pentanediol, 0.1M (2-(N-morpholino)ethanesulfonic acid)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→57.65 Å / Num. obs: 67976 / % possible obs: 97.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 9.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.7
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 7.2 / CC1/2: 0.945 / % possible all: 83.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→32.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.042 / SU Rfree Blow DPI: 0.042 / SU Rfree Cruickshank DPI: 0.04
RfactorNum. reflection% reflectionSelection details
Rfree0.176 3358 4.94 %RANDOM
Rwork0.164 ---
obs0.165 67974 97.2 %-
Displacement parametersBiso mean: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.0358 Å20 Å20.3348 Å2
2--0.4666 Å20 Å2
3----0.4308 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: 1 / Resolution: 1.2→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 42 289 2217
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092158HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.132970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d785SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes338HARMONIC5
X-RAY DIFFRACTIONt_it2158HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.09
X-RAY DIFFRACTIONt_other_torsion14.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion274SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2970SEMIHARMONIC4
LS refinement shellResolution: 1.2→1.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 200 5.19 %
Rwork0.168 3656 -
all0.169 3856 -
obs--75.49 %
Refinement TLS params.Method: refined / Origin x: 24.6633 Å / Origin y: 1.679 Å / Origin z: 42.1359 Å
111213212223313233
T-0.0169 Å20.0039 Å2-0.0039 Å2--0.0221 Å20.0048 Å2---0.0194 Å2
L0.5388 °2-0.0827 °2-0.2575 °2-0.3476 °20.2044 °2--0.6634 °2
S-0.021 Å °-0.0366 Å °-0.0175 Å °0.0144 Å °0.0112 Å °-0.0032 Å °-0.0022 Å °0.0249 Å °0.0098 Å °
Refinement TLS groupSelection details: { A|* }

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