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- PDB-6shh: Human kallikrein 7 with aromatic coumarinic ester compound 1 cova... -

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Basic information

Entry
Database: PDB / ID: 6shh
TitleHuman kallikrein 7 with aromatic coumarinic ester compound 1 covalently bound to H57
ComponentsKallikrein-7
KeywordsHYDROLASE / Serine Protease / Covalent Inhibitor / Complex
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / protein maturation ...stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / protein maturation / 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 / 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
TRIETHYLENE GLYCOL / Chem-SH7 / Kallikrein-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHanke, S. / Straeter, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC 1052 - project C4 Germany
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
DepositionAug 6, 2019Deposition 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: Kallikrein-7
E: Kallikrein-7
F: Kallikrein-7
G: Kallikrein-7
H: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,418105
Polymers195,8498
Non-polymers11,56897
Water20,6991149
1
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,81112
Polymers24,4811
Non-polymers1,32911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,04515
Polymers24,4811
Non-polymers1,56414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,04515
Polymers24,4811
Non-polymers1,56414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,90713
Polymers24,4811
Non-polymers1,42612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,71511
Polymers24,4811
Non-polymers1,23310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,90713
Polymers24,4811
Non-polymers1,42612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,89912
Polymers24,4811
Non-polymers1,41811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,09114
Polymers24,4811
Non-polymers1,61013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.630, 116.410, 290.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 24481.160 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The inhibitor is covalently attached to H57 / Source: (gene. exp.) Homo sapiens (human) / Gene: KLK7, PRSS6, SCCE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: P49862, stratum corneum chymotryptic enzyme

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Non-polymers , 5 types, 1246 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 83 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SH7 / (3-chlorophenyl) 6-methyl-2-oxidanylidene-chromene-3-carboxylate


Mass: 314.720 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H11ClO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2.9 M ammonium sulphate, 0.1 M HEPES, pH 8.5, 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: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→48.49 Å / Num. obs: 138723 / % possible obs: 99.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 30.04 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.166 / Rrim(I) all: 0.37 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 8.5 % / Rmerge(I) obs: 4.121 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5745 / CC1/2: 0.229 / Rrim(I) all: 4.638 / % possible all: 84.1

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qxi

2qxi


Resolution: 2→47.03 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2106 1.52 %RANDOM
Rwork0.189 ---
obs0.19 138570 99.2 %-
Displacement parametersBiso max: 171.15 Å2 / Biso mean: 43.07 Å2 / Biso min: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.9598 Å20 Å20 Å2
2---10.7956 Å20 Å2
3---7.8358 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13629 0 541 1149 15319
Biso mean--84.65 45.6 -
Num. residues----1792
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4841SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2733HARMONIC5
X-RAY DIFFRACTIONt_it14732HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1826SEMIHARMONIC5
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_contact16992SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14732HARMONIC20.012
X-RAY DIFFRACTIONt_angle_deg20215HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion17.2
LS refinement shellResolution: 2→2.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3287 33 1.19 %
Rwork0.2497 2739 -
all0.2506 2772 -
obs--72.95 %
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)
11.12230.2047-0.00510.92920.02591.0859-0.0369-0.03830.02530.0683-0.00230.01490.0066-0.13360.0392-0.0221-0.004-0.0020.2383-0.0109-0.0055-20.297-16.348964.3344
21.72830.05430.09471.2675-0.01171.1867-0.0293-0.0470.0144-0.01040.00150.0282-0.045-00.0278-0.1415-0.0113-0.00660.1105-0.0182-0.11462.494-5.981949.2384
31.2740.20010.24961.00280.30681.7383-0.02680.00780.0388-0.0583-0.0192-0.0187-0.1743-0.08160.0459-0.15130.008-0.0120.1483-0.0142-0.118-28.9673-4.504228.5318
41.80860.40480.44151.90010.30051.61850.04960.0611-0.15810.1276-0.0087-0.10570.13720.0927-0.0409-0.0508-0.0053-0.00590.0842-0.0201-0.09362.03284.882186.8731
51.47810.020.37360.8968-0.06991.5761-0.1046-0.00870.0309-0.07020.05560.0097-0.09560.14110.049-0.0522-0.0129-0.00390.2417-0.0091-0.0399-6.1637-12.894312.37
61.66270.16290.33640.890.26241.5932-0.07440.04-0.071-0.10670.0412-0.03980.0358-0.05170.0332-0.0157-0.00070.02440.14530.0024-0.0625-9.721212.7803122.213
71.59070.18640.2382.52360.15632.3860.0974-0.08660.1143-0.0635-0.1570.1056-0.51950.00930.0596-0.04020.0305-0.00060.0456-0.003-0.2146-29.90029.8587-7.1714
81.3943-0.0318-0.12341.94760.62012.05020.0241-0.037-0.03030.25720.0008-0.10290.4612-0.0517-0.02490.0536-0.0266-0.0496-0.0539-0.0091-0.1942-7.9851-18.5961101.073
900.0820.22270.1355-0.02810.78290.03290.0154-0.00210.0233-0.00440.02490.0023-0.0465-0.0285-0.2110.0114-0.02020.401-0.0029-0.141-15.0137-0.35759.1014
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
4X-RAY DIFFRACTION4{ D|* }D16 - 246
5X-RAY DIFFRACTION5{ E|* }E16 - 246
6X-RAY DIFFRACTION6{ F|* }F16 - 246
7X-RAY DIFFRACTION7{ G|* }G16 - 246
8X-RAY DIFFRACTION8{ H|* }H16 - 246
9X-RAY DIFFRACTION9{ A|301 }A301

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