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- PDB-6o1s: Structure of human plasma kallikrein protease domain with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6o1s
TitleStructure of human plasma kallikrein protease domain with inhibitor
ComponentsPlasma kallikrein
KeywordsBLOOD CLOTTING / Protease
Function / homology
Function and homology information


plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple 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 ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple 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-7SD / PHOSPHATE ION / Plasma kallikrein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPartridge, J.R. / Choy, R.M.
Citation
Journal: J.Struct.Biol. / Year: 2019
Title: Structures of full-length plasma kallikrein bound to highly specific inhibitors describe a new mode of targeted inhibition.
Authors: Partridge, J.R. / Choy, R.M. / Silva-Garcia, A. / Yu, C. / Li, Z. / Sham, H. / Metcalf, B.
#1: Journal: ACS Med Chem Lett / Year: 2017
Title: Structure-Guided Design of Novel, Potent, and Selective Macrocyclic Plasma Kallikrein Inhibitors.
Authors: Li, Z. / Partridge, J. / Silva-Garcia, A. / Rademacher, P. / Betz, A. / Xu, Q. / Sham, H. / Hu, Y. / Shan, Y. / Liu, B. / Zhang, Y. / Shi, H. / Xu, Q. / Ma, X. / Zhang, L.
History
DepositionFeb 21, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2019ID: 5TZ9
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Plasma kallikrein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0004
Polymers29,4271
Non-polymers5733
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.685, 57.450, 86.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plasma kallikrein / Fletcher factor / Kininogenin / Plasma prekallikrein / PKK


Mass: 29427.314 Da / Num. of mol.: 1 / Mutation: N377E, N434E, N475E, C383E, and C484S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLKB1, KLK3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03952, plasma kallikrein
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7SD / N-[(6-amino-2,4-dimethylpyridin-3-yl)methyl]-1-({4-[(1H-pyrazol-1-yl)methyl]phenyl}methyl)-1H-pyrazole-4-carboxamide


Mass: 415.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N7O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 24% PEG 3350, 0.2M potassium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 31089 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 21.9 Å2 / Rpim(I) all: 0.032 / Rsym value: 0.092 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 4.1 / Rpim(I) all: 0.339 / Rsym value: 0.977 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANW

2anw


Resolution: 1.7→27.842 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 2000 6.43 %
Rwork0.1699 --
obs0.1719 31089 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 40 208 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062005
X-RAY DIFFRACTIONf_angle_d0.7352725
X-RAY DIFFRACTIONf_dihedral_angle_d12.421172
X-RAY DIFFRACTIONf_chiral_restr0.055285
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.22431460.19592048X-RAY DIFFRACTION100
1.7425-1.78960.24481380.19382040X-RAY DIFFRACTION100
1.7896-1.84230.28041450.21292034X-RAY DIFFRACTION100
1.8423-1.90170.21171350.19942073X-RAY DIFFRACTION100
1.9017-1.96970.22511450.18162035X-RAY DIFFRACTION100
1.9697-2.04850.22341450.17612055X-RAY DIFFRACTION100
2.0485-2.14170.21221380.17282068X-RAY DIFFRACTION100
2.1417-2.25460.21221350.17992055X-RAY DIFFRACTION100
2.2546-2.39580.17691460.17162078X-RAY DIFFRACTION100
2.3958-2.58060.19571360.17162070X-RAY DIFFRACTION100
2.5806-2.84010.22091440.18152090X-RAY DIFFRACTION100
2.8401-3.25060.21531430.17992091X-RAY DIFFRACTION100
3.2506-4.09330.19211480.15282130X-RAY DIFFRACTION100
4.0933-27.84620.17241560.15312222X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.9546 Å / Origin y: -9.5999 Å / Origin z: 13.7136 Å
111213212223313233
T0.1709 Å20.0225 Å2-0.0011 Å2-0.1625 Å20.0011 Å2--0.1359 Å2
L3.5872 °2-0.8132 °20.3508 °2-2.9472 °21.1712 °2--2.6475 °2
S-0.1992 Å °-0.2931 Å °-0.1408 Å °0.1908 Å °0.3253 Å °-0.0816 Å °-0.0232 Å °0.2402 Å °-0.0655 Å °
Refinement TLS groupSelection details: all

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