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- PDB-6sju: Human kallikrein 7 with aromatic coumarinic ester compound 3 cova... -

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Basic information

Entry
Database: PDB / ID: 6sju
TitleHuman kallikrein 7 with aromatic coumarinic ester compound 3 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 / secretory granule ...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 / 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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Chem-LFW / TRIETHYLENE GLYCOL / Kallikrein-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 13, 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

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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)209,122114
Polymers195,8498
Non-polymers13,273106
Water25,8151433
1
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,05213
Polymers24,4811
Non-polymers1,57112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,19015
Polymers24,4811
Non-polymers1,70914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,32817
Polymers24,4811
Non-polymers1,84716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,19015
Polymers24,4811
Non-polymers1,70914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,90212
Polymers24,4811
Non-polymers1,42111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,09414
Polymers24,4811
Non-polymers1,61313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,84812
Polymers24,4811
Non-polymers1,36711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,51716
Polymers24,4811
Non-polymers2,03615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.650, 116.950, 291.190
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 (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: P49862, stratum corneum chymotryptic enzyme

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Non-polymers , 5 types, 1539 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-LFW / (3-iodanylphenyl) 6-methyl-2-oxidanylidene-chromene-3-carboxylate


Mass: 406.171 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H11IO4
#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.: 1433 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: 2.101 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: 2.101 Å / Relative weight: 1
ReflectionResolution: 1.97→47.08 Å / Num. obs: 115901 / % possible obs: 78.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 38.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.097 / Χ2: 1.01 / Net I/σ(I): 16.2
Reflection shellResolution: 1.97→2 Å / Redundancy: 3 % / Rmerge(I) obs: 1.743 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 869 / CC1/2: 0.042 / Rrim(I) all: 2.268 / Χ2: 0.98 / % possible all: 12.2

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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: 1.97→47.08 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1719 1.48 %RANDOM
Rwork0.174 ---
obs0.175 115848 78.4 %-
Displacement parametersBiso max: 199.47 Å2 / Biso mean: 44.11 Å2 / Biso min: 22.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.8692 Å20 Å20 Å2
2---8.398 Å20 Å2
3---7.5288 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.97→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13629 0 641 1433 15703
Biso mean--79.14 53.55 -
Num. residues----1792
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4860SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2733HARMONIC5
X-RAY DIFFRACTIONt_it14823HARMONIC20
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_contact17160SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14823HARMONIC20.013
X-RAY DIFFRACTIONt_angle_deg20378HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion15.93
LS refinement shellResolution: 1.97→2.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2509 30 1.29 %
Rwork0.2538 2287 -
all0.2538 2317 -
obs--16.67 %
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)
11.3102-0.02620.06151.10560.14490.9847-0.0046-0.02390.02180.07-0.00810.00540.0288-0.09390.01270.2166-0.0162-0.00480.27-0.00320.2264-20.1196-16.210864.6062
21.53570.06020.19881.1233-0.10321.1578-0.0106-0.00760.0272-0.022-0.02490.0217-0.0067-0.00070.03540.2173-0.0087-0.00180.2879-0.02080.24222.4139-5.916749.0707
31.30490.14750.32681.19210.46931.5094-0.0249-0.02580.0081-0.051-0.0225-0.0275-0.1291-0.09660.0475-0.0870.0101-0.00860.0035-0.0072-0.0702-28.9202-4.601428.4995
41.62240.50110.50811.91970.37521.38720.09410.0414-0.19830.1472-0.0242-0.16750.13640.0535-0.06990.0847-0.01-0.01610.0295-0.0190.04322.02915.042486.9198
51.46320.25220.14451.1399-0.30461.3438-0.09070.0554-0.0038-0.0420.06080.0206-0.05330.14540.02990.0546-0.0022-0.00070.1326-0.00820.0413-6.1338-12.991812.3867
61.69150.27070.42680.98770.30561.2155-0.09080.0536-0.0656-0.14750.0538-0.05460.0222-0.07140.0370.2971-0.00860.02240.2425-0.00720.2278-9.758312.9471122.278
71.24860.33730.30732.63880.10622.14810.0924-0.05810.0628-0.0669-0.12990.1436-0.4203-0.06680.03760.01250.03980.0075-0.09570.0018-0.1331-29.83489.6128-7.094
81.5536-0.2083-0.05672.4050.57612.08250.0071-0.0541-0.01420.26410.0153-0.14640.4037-0.0521-0.02240.4879-0.0355-0.06070.1878-0.00120.2407-7.9943-18.2543101.425
90.0550.04220.16490.18830.10370.6460.00730.02850.00090.0083-0.00480.0513-0.0214-0.087-0.0025-0.1227-0.013-0.0241-0.00650.00310.0243-16.15320.785259.4136
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{ I|* }I1 - 108

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