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- PDB-5f8x: The crystal structure of human plasma kallikrein in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5f8x
TitleThe crystal structure of human plasma kallikrein in complex with its peptide inhibitor pkalin-3
Components
  • CYS-PRO-ALA-ARG-PHE-M70-ALA-LEU-TRP-CYS
  • Plasma kallikrein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PEPTIDE 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
piperidine-1-carboximidamide / Plasma kallikrein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsXu, M. / Jiang, L. / Xu, P. / Luo, Z. / Andreasen, P. / Huang, M.
CitationJournal: To Be Published
Title: The Crystal Structure Of Human Plasma Kallikrein In Complex With Its Peptide Inhibitor Pkalin-3
Authors: Xu, M. / Jiang, L. / Xu, P. / Luo, Z. / Andreasen, P. / Huang, M.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 14, 2016ID: 4ZJ6
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasma kallikrein
B: CYS-PRO-ALA-ARG-PHE-M70-ALA-LEU-TRP-CYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,94811
Polymers28,0522
Non-polymers8969
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-123 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.339, 90.339, 57.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 26913.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 391-629 / Mutation: C122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLKB1, KLK3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P03952, plasma kallikrein
#2: Protein/peptide CYS-PRO-ALA-ARG-PHE-M70-ALA-LEU-TRP-CYS


Mass: 1138.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MRZ / piperidine-1-carboximidamide


Mass: 127.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 23% PEG 3350, 0.1M TRIS-HCL, PH 8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 38722 / % possible obs: 100 % / Redundancy: 5.5 % / Net I/σ(I): 26.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANY

2any


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.729 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1939 5 %RANDOM
Rwork0.221 ---
obs0.222 36754 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 49 195 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022038
X-RAY DIFFRACTIONr_bond_other_d0.0010.021878
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9622737
X-RAY DIFFRACTIONr_angle_other_deg0.74234317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65425.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58215340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.545156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
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_it0.8862.051968
X-RAY DIFFRACTIONr_mcbond_other0.8862.05967
X-RAY DIFFRACTIONr_mcangle_it1.573.0451168
X-RAY DIFFRACTIONr_mcangle_other1.5693.0461169
X-RAY DIFFRACTIONr_scbond_it0.8772.2331070
X-RAY DIFFRACTIONr_scbond_other0.8212.1621034
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3493.2011516
X-RAY DIFFRACTIONr_long_range_B_refined4.80118.0892539
X-RAY DIFFRACTIONr_long_range_B_other4.25617.3812427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 146 -
Rwork0.266 2642 -
obs--98.8 %

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