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- PDB-6qfg: Crystal Structure of Human Kallikrein 6 (I218Y) in complex with GSK144 -

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Basic information

Entry
Database: PDB / ID: 6qfg
TitleCrystal Structure of Human Kallikrein 6 (I218Y) in complex with GSK144
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
Chem-J08 / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsThorpe, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Evaluation of a crystallographic surrogate for kallikrein 5 in the discovery of novel inhibitors for Netherton syndrome.
Authors: Thorpe, J.H. / Edgar, E.V. / Smith, K.J. / Lewell, X.Q. / Rella, M. / White, G.V. / Polyakova, O. / Nassau, P. / Walker, A.L. / Holmes, D.S. / Pearce, A.C. / Wang, Y. / Liddle, J. / Hovnanian, A.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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)49,9176
Polymers48,9352
Non-polymers9814
Water6,305350
1
A: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9583
Polymers24,4681
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9583
Polymers24,4681
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.400, 45.900, 89.350
Angle α, β, γ (deg.)90.000, 93.640, 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: R74G/R76Q/N132Q/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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-J08 / 4-[(5-phenyl-1~{H}-imidazol-2-yl)methylamino]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide


Mass: 398.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.68→58.32 Å / Num. obs: 51138 / % possible obs: 94.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 28.11 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Rrim(I) all: 0.047 / Net I/σ(I): 12.4 / Num. measured all: 145045 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.68-1.721.70.43425050.620.3870.58463.6
7.51-58.323.10.036600.9320.0220.03799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LO6

1lo6


Resolution: 1.68→58.29 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2454 4.8 %RANDOM
Rwork0.191 ---
obs0.193 51113 94.2 %-
Displacement parametersBiso max: 114.92 Å2 / Biso mean: 31.23 Å2 / Biso min: 14.95 Å2
Baniso -1Baniso -2Baniso -3
1-4.1892 Å20 Å25.274 Å2
2---3.9401 Å20 Å2
3----0.2491 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.68→58.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 72 350 3837
Biso mean--32.15 40.99 -
Num. residues----445
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1203SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes526HARMONIC5
X-RAY DIFFRACTIONt_it3607HARMONIC20
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_contact4267SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3607HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4909HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.62
LS refinement shellResolution: 1.68→1.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 129 5.15 %
Rwork0.223 2376 -
all0.2229 2505 -
obs--62.56 %

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