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- PDB-6o1g: Full length human plasma kallikrein with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6o1g
TitleFull length human plasma kallikrein 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-7SD / Plasma kallikrein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPartridge, J.R. / Choy, R.M.
CitationJournal: 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.
History
DepositionFeb 19, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2019ID: 6ESO
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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasma kallikrein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3114
Polymers71,4531
Non-polymers8583
Water2,504139
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)55.970, 121.920, 65.890
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 71452.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P03952, plasma kallikrein
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes pH 7.5 0.1 M Sodium Citrate 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127131 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127131 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 37739 / % possible obs: 88 % / Redundancy: 2.1 % / Biso Wilson estimate: 30.93 Å2 / Net I/σ(I): 2.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.1 % / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.126 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28
RfactorNum. reflection% reflection
Rfree0.2401 2000 5.3 %
Rwork0.2006 --
obs0.2027 37739 87.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 59 139 4793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084783
X-RAY DIFFRACTIONf_angle_d0.9036485
X-RAY DIFFRACTIONf_dihedral_angle_d14.1892869
X-RAY DIFFRACTIONf_chiral_restr0.055708
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.3241360.29292429X-RAY DIFFRACTION83
2.255-2.31590.34341350.2692410X-RAY DIFFRACTION83
2.3159-2.38410.33911370.26332450X-RAY DIFFRACTION84
2.3841-2.4610.28651370.24452438X-RAY DIFFRACTION84
2.461-2.54890.29941370.2472467X-RAY DIFFRACTION85
2.5489-2.65080.30851380.25152457X-RAY DIFFRACTION85
2.6508-2.77140.34671380.2422474X-RAY DIFFRACTION85
2.7714-2.91740.28621390.24242467X-RAY DIFFRACTION85
2.9174-3.09990.24981390.23032511X-RAY DIFFRACTION86
3.0999-3.33890.22781420.2062523X-RAY DIFFRACTION87
3.3389-3.67430.23031480.18712650X-RAY DIFFRACTION90
3.6743-4.20440.22881550.16672772X-RAY DIFFRACTION95
4.2044-5.29140.18121570.14932789X-RAY DIFFRACTION95
5.2914-28.12820.17661620.17312902X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -39.238 Å / Origin y: -10.2102 Å / Origin z: 24.6158 Å
111213212223313233
T0.2228 Å2-0.0047 Å20.0282 Å2-0.2408 Å2-0.0165 Å2--0.2645 Å2
L0.8571 °20.2088 °20.06 °2-1.8348 °20.0773 °2--0.4861 °2
S0.0247 Å °-0.0408 Å °0.2163 Å °0.066 Å °-0.0316 Å °0.2409 Å °-0.1998 Å °0.0183 Å °0.0097 Å °
Refinement TLS groupSelection details: all

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