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- PDB-5tjx: Structure of human plasma kallikrein -

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Basic information

Entry
Database: PDB / ID: 5tjx
TitleStructure of human plasma kallikrein
ComponentsPlasma kallikrein
KeywordsHydrolase/Hydrolase Inhibitor / plasma kallikrein / protease / serine / inhibitor / Hydrolase-Hydrolase Inhibitor complex
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 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-GBT / PHOSPHATE ION / Plasma kallikrein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.408 Å
AuthorsPartridge, J.R. / Choy, R.M. / Li, Z.
CitationJournal: 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
DepositionOct 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Oct 4, 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 1.3Oct 23, 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
A: Plasma kallikrein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1454
Polymers29,4271
Non-polymers7183
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.660, 59.620, 77.110
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 / Fragment: UNP residues 376-638 / Mutation: N396E, N453E, N494E, C503S
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-GBT / (8E)-3-amino-1-methyl-15-[(1H-pyrazol-1-yl)methyl]-7,10,11,12,24,25-hexahydro-6H,18H,23H-19,22-(metheno)pyrido[4,3-j][1,9,13,17,18]benzodioxatriazacyclohenicosin-23-one


Mass: 527.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N7O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium di-hydrogen phosphate, 21 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.408→30 Å / Num. obs: 48771 / % possible obs: 96.81 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.86 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.057 / Net I/σ(I): 13.26
Reflection shellResolution: 1.408→1.458 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2132 / Mean I/σ(I) obs: 3.48 / CC1/2: 0.862 / % possible all: 94.82

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2any

2any


Resolution: 1.408→27.805 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.94
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 1988 4.08 %Random selection
Rwork0.1626 ---
obs0.1634 48757 96.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.408→27.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 49 334 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061967
X-RAY DIFFRACTIONf_angle_d0.8842675
X-RAY DIFFRACTIONf_dihedral_angle_d20.239728
X-RAY DIFFRACTIONf_chiral_restr0.077278
X-RAY DIFFRACTIONf_plane_restr0.005335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.408-1.44320.22241310.21563213X-RAY DIFFRACTION95
1.4432-1.48220.22121420.19243273X-RAY DIFFRACTION96
1.4822-1.52590.23031380.17733265X-RAY DIFFRACTION96
1.5259-1.57510.19281360.17653300X-RAY DIFFRACTION96
1.5751-1.63140.22681510.1663265X-RAY DIFFRACTION96
1.6314-1.69670.2021380.15453271X-RAY DIFFRACTION96
1.6967-1.77390.15151470.1543281X-RAY DIFFRACTION96
1.7739-1.86740.16081320.15573280X-RAY DIFFRACTION95
1.8674-1.98440.17741470.15873310X-RAY DIFFRACTION96
1.9844-2.13750.1621360.15363364X-RAY DIFFRACTION97
2.1375-2.35260.1981360.16223441X-RAY DIFFRACTION99
2.3526-2.69270.15451530.17073470X-RAY DIFFRACTION100
2.6927-3.39160.19961480.15923477X-RAY DIFFRACTION99
3.3916-27.810.18451530.15773559X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -17.2718 Å / Origin y: 7.8646 Å / Origin z: -12.7873 Å
111213212223313233
T0.0804 Å20.0011 Å2-0.0033 Å2-0.0575 Å2-0.0073 Å2--0.0663 Å2
L1.7664 °20.0487 °2-0.0414 °2-1.1098 °20.3032 °2--1.0443 °2
S0.0057 Å °0.0729 Å °-0.083 Å °-0.0144 Å °0.0167 Å °-0.0704 Å °0.0437 Å °0.0307 Å °-0.0105 Å °
Refinement TLS groupSelection details: all

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