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- PDB-6qhc: Crystal Structure of Human Kallikrein 6 in complex with GSK358180B -

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Basic information

Entry
Database: PDB / ID: 6qhc
TitleCrystal Structure of Human Kallikrein 6 in complex with GSK358180B
ComponentsKallikrein-6
KeywordsHYDROLASE / Protease / Inhibitor / Complex
Function / homology
Function and homology information


cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid precursor protein metabolic process / hormone metabolic process / regulation of neuron projection development / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid precursor protein metabolic process / hormone metabolic process / regulation of neuron projection development / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / intercellular bridge / myelination / secretory granule / protein maturation / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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
N-(4-CARBAMIMIDOYL-PHENYL)-2-HYDROXY-BENZAMIDE / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsThorpe, J.H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2019
Title: Kallikrein 5 inhibitors identified through structure based drug design in search for a treatment for Netherton Syndrome.
Authors: White, G.V. / Edgar, E.V. / Holmes, D.S. / Lewell, X.Q. / Liddle, J. / Polyakova, O. / Smith, K.J. / Thorpe, J.H. / Walker, A.L. / Wang, Y. / Young, R.J. / Hovnanian, A.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Revision 1.3Oct 16, 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: Kallikrein-6
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5166
Polymers48,8352
Non-polymers6814
Water3,891216
1
A: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7653
Polymers24,4181
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7513
Polymers24,4181
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.680, 45.730, 89.580
Angle α, β, γ (deg.)90.00, 93.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24417.695 Da / Num. of mol.: 2 / Mutation: R74G/R76Q/N132Q
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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-135 / N-(4-CARBAMIMIDOYL-PHENYL)-2-HYDROXY-BENZAMIDE


Mass: 255.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→34.38 Å / Num. obs: 36020 / % possible obs: 92.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.095 / Net I/σ(I): 9.1
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2655 / CC1/2: 0.832 / Rrim(I) all: 0.477 / % possible all: 68.87

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimless0.2.12data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LO6

1lo6


Resolution: 1.87→17.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.161 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1796 4.99 %RANDOM
Rwork0.199 ---
obs0.201 36020 92.6 %-
Displacement parametersBiso mean: 32.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.544 Å20 Å20.7087 Å2
2--0.0768 Å20 Å2
3----0.6208 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.87→17.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 48 216 3662
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013565HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.134856HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1190SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes522HARMONIC5
X-RAY DIFFRACTIONt_it3565HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion16.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
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_contact4150SEMIHARMONIC4
LS refinement shellResolution: 1.87→1.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.342 -4.22 %
Rwork0.266 2022 -
all0.269 2111 -
obs--66.41 %

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