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- PDB-6y4s: Human kallikrein-related peptidase 7 (KLK7) in the unliganded state -

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Basic information

Entry
Database: PDB / ID: 6y4s
TitleHuman kallikrein-related peptidase 7 (KLK7) in the unliganded state
ComponentsKallikrein-7
KeywordsHYDROLASE / kallikrein 7 / hK7 / serine protease
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / metalloendopeptidase activity ...stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / metalloendopeptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
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
TRIETHYLENE GLYCOL / Kallikrein-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.23 Å
Model detailsThe compound is a competitive non-nucleotide inhibitor binding to the active site
AuthorsHanke, S. / Strater, N.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Studies on the Inhibitory Binding Mode of Aromatic Coumarinic Esters to Human Kallikrein-Related Peptidase 7.
Authors: Hanke, S. / Tindall, C.A. / Pippel, J. / Ulbricht, D. / Pirotte, B. / Reboud-Ravaux, M. / Heiker, J.T. / Strater, N.
History
DepositionFeb 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
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

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-7
B: Kallikrein-7
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,93918
Polymers73,4433
Non-polymers1,49515
Water1,47782
1
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2088
Polymers24,4811
Non-polymers7277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7694
Polymers24,4811
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9616
Polymers24,4811
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.150, 113.150, 326.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Kallikrein-7 / hK7 / Serine protease 6 / Stratum corneum chymotryptic enzyme / hSCCE


Mass: 24481.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK7, PRSS6, SCCE / Production host: Escherichia coli (E. coli)
References: UniProt: P49862, stratum corneum chymotryptic enzyme
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.9 M ammonium sulphate, 0.1 M HEPES, pH 8.5 and 0.5-2 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.23→48.45 Å / Num. obs: 39789 / % possible obs: 99.8 % / Redundancy: 15 % / Biso Wilson estimate: 40.47 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.436 / Rpim(I) all: 0.116 / Rrim(I) all: 0.452 / Net I/σ(I): 6.3 / Num. measured all: 596786
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.23-2.313.76.4774831835260.2961.7926.7280.597.6
8.9-48.4512.50.05387677010.9990.0160.05630.799

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3bsq

3bsq


Resolution: 2.23→48.45 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2041 5.13 %RANDOM
Rwork0.219 ---
obs0.22 39785 99.7 %-
Displacement parametersBiso max: 172.92 Å2 / Biso mean: 56.26 Å2 / Biso min: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1--7.5986 Å20 Å20 Å2
2---7.5986 Å20 Å2
3---15.1973 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.23→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 0 80 82 5277
Biso mean--90.35 46.01 -
Num. residues----672
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1804SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes870HARMONIC5
X-RAY DIFFRACTIONt_it5312HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion684SEMIHARMONIC5
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_contact5738SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5312HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7223HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion16.62
LS refinement shellResolution: 2.23→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2611 41 5.15 %
Rwork0.2353 755 -
all0.2368 796 -
obs--88.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0464-1.38790.08652.4829-0.16342.62070.00540.17560.0901-0.1881-0.0637-0.13530.1987-0.03270.0584-0.05790.06270.0093-0.1133-0.0027-0.2018-41.166516.06129.4718
21.84520.3456-0.48341.6822-0.0443.31970.0344-0.0207-0.03960.01440.01630.05880.3447-0.356-0.0507-0.08670.0228-0.0223-0.0322-0.0048-0.1618-22.572-7.526743.4621
33.05560.2493-0.14926.0895-2.71187.93480.10640.0234-0.1243-0.4765-0.4912-0.38750.57210.28710.3849-0.10430.1320.0427-0.11740.0472-0.3701-29.424-15.08556.8862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A16 - 246
2X-RAY DIFFRACTION2{ B|* }B16 - 246
3X-RAY DIFFRACTION3{ C|* }C16 - 246

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