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- PDB-6skc: Crystal Structure of Human Kallikrein 6 (I218Y) in complex with G... -

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Basic information

Entry
Database: PDB / ID: 6skc
TitleCrystal Structure of Human Kallikrein 6 (I218Y) in complex with GSK3448330A
ComponentsKallikrein-6KLK6
KeywordsHYDROLASE / Protease / Inhibitor / Complex
Function / homology
Function and homology information


tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm
Similarity search - Function
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 ...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
BENZAMIDINE / Chem-LH8 / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsThorpe, J.H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Design and development of a series of borocycles as selective, covalent kallikrein 5 inhibitors.
Authors: Walker, A.L. / Denis, A. / Bingham, R.P. / Boulliot, A. / Edgar, E.V. / Ferrie, A. / Holmes, D.S. / Laroze, A. / Liddle, J. / Fouchet, M.H. / Moquette, A. / Nassau, P. / Pearce, A.C. / ...Authors: Walker, A.L. / Denis, A. / Bingham, R.P. / Boulliot, A. / Edgar, E.V. / Ferrie, A. / Holmes, D.S. / Laroze, A. / Liddle, J. / Fouchet, M.H. / Moquette, A. / Nassau, P. / Pearce, A.C. / Polyakova, O. / Smith, K.J. / Thomas, P. / Thorpe, J.H. / Trottet, L. / Wang, Y. / Hovnanian, A.
History
DepositionAug 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Kallikrein-6
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4145
Polymers48,9352
Non-polymers4783
Water2,792155
1
A: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7342
Polymers24,4681
Non-polymers2661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6803
Polymers24,4681
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.080, 46.080, 80.960
Angle α, β, γ (deg.)90.000, 98.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-6 / KLK6 / Neurosin / Protease M / SP59 / Serine protease 18 / Serine protease 9 / Zyme


Mass: 24467.711 Da / Num. of mol.: 2 / Mutation: I218Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-LH8 / 4-[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]benzenecarboximidamide


Mass: 266.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15BN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 / Details: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.18→35.94 Å / Num. obs: 66928 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 39.24 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.081 / Rrim(I) all: 0.146 / Net I/σ(I): 6.5
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4905 / CC1/2: 0.804 / Rpim(I) all: 0.399 / Rrim(I) all: 0.565 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LO6

1lo6


Resolution: 2.18→35.44 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1065 4.83 %RANDOM
Rwork0.188 ---
obs0.19 22071 98.5 %-
Displacement parametersBiso max: 101.09 Å2 / Biso mean: 35.31 Å2 / Biso min: 15.89 Å2
Baniso -1Baniso -2Baniso -3
1-8.9424 Å20 Å24.5103 Å2
2---4.9001 Å20 Å2
3----4.0423 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.18→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 35 155 3596
Biso mean--40.84 36.16 -
Num. residues----444
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1188SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes605HARMONIC5
X-RAY DIFFRACTIONt_it3555HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
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_contact3859SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3555HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4840HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion17.84
LS refinement shellResolution: 2.18→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2157 18 4.07 %
Rwork0.1996 424 -
all0.2002 442 -
obs--98.7 %

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