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- PDB-6shi: Human kallikrein 7 with aromatic coumarinic ester compound 2 cova... -

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Basic information

Entry
Database: PDB / ID: 6shi
TitleHuman kallikrein 7 with aromatic coumarinic ester compound 2 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 / 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 / Chem-SH8 / Kallikrein-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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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)206,917109
Polymers195,8498
Non-polymers11,068101
Water33,9941887
1
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,79613
Polymers24,4811
Non-polymers1,31512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,98815
Polymers24,4811
Non-polymers1,50714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,83814
Polymers24,4811
Non-polymers1,35713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,89214
Polymers24,4811
Non-polymers1,41113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,45410
Polymers24,4811
Non-polymers9739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,89214
Polymers24,4811
Non-polymers1,41113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,98014
Polymers24,4811
Non-polymers1,49913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,07615
Polymers24,4811
Non-polymers1,59514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.640, 116.964, 291.268
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, 1988 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-SH8 / 6-methyl-2-oxidanylidene-chromene-3-carboxylic acid


Mass: 204.179 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H8O4
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 87 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


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


Mass: 18.015 Da / Num. of mol.: 1887 / 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: 53.65 %
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: 0.920172 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: 0.920172 Å / Relative weight: 1
ReflectionResolution: 1.85→47.08 Å / Num. obs: 177629 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.169 / Χ2: 1.01 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.823 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8592 / CC1/2: 0.423 / Rrim(I) all: 2.119 / Χ2: 1.01 / % possible all: 98.7

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Processing

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

2qxi


Resolution: 1.85→46.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.137 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2682 1.51 %RANDOM
Rwork0.176 ---
obs0.176 177508 99.8 %-
Displacement parametersBiso max: 204.2 Å2 / Biso mean: 33.78 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.1557 Å20 Å20 Å2
2---6.2293 Å20 Å2
3---6.0736 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.85→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13629 0 561 1887 16077
Biso mean--70.69 45.27 -
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_it14748HARMONIC20
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_contact17617SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14748HARMONIC20.013
X-RAY DIFFRACTIONt_angle_deg20239HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion15.06
LS refinement shellResolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.297 44 1.24 %
Rwork0.2322 3507 -
all0.233 3551 -
obs--99.19 %
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)
11.3020.03270.10330.94380.08720.9949-0.0101-0.00250.0360.0496-0.00780.00990.0116-0.09010.018-0.0027-0.0144-0.00150.0456-0.00540.0042-20.186-16.36264.4425
21.51570.12490.23311.01-0.06571.1139-0.0061-0.03870.0188-0.0084-0.02610.0272-0.0307-0.00680.0322-0.0707-0.0123-0.0013-0.0033-0.0181-0.05232.5616-6.055949.2914
31.18190.0860.34931.20220.40711.5551-0.0248-0.01730.0195-0.0593-0.0299-0.0278-0.1382-0.09220.0547-0.07740.0107-0.00810.0093-0.0066-0.0664-28.9185-4.647728.536
41.43970.56240.5251.89910.37191.1910.07950.0538-0.16230.1615-0.0209-0.13050.1270.055-0.05850.0703-0.0076-0.01390.0206-0.01770.02612.04674.983286.9454
51.63530.27450.21991.0631-0.23521.3137-0.1060.05260.0051-0.05460.06280.0067-0.07020.14510.04320.0323-0.00450.0010.0979-0.00650.0065-6.1386-13.0112.3898
61.51470.25470.34431.03620.31811.2192-0.09440.0286-0.0584-0.14050.049-0.04330.0415-0.06660.04540.1266-0.00910.01750.0753-0.00640.0544-9.735212.9213122.333
71.23430.23970.30632.53380.09491.93560.0975-0.05620.0592-0.0838-0.13720.116-0.4097-0.05590.03970.01890.04280.0047-0.08510.0001-0.1273-29.82749.6739-7.193
81.428-0.0445-0.0182.25480.61691.89150.0086-0.02910.00040.25620.0034-0.12780.42-0.0529-0.0120.1198-0.0351-0.055-0.16970.0004-0.1333-7.9172-18.4738101.211
900.10330.15810.1570.05680.57560.00850.00390.02110.04060.00190.0519-0.0236-0.1308-0.0104-0.11980.0038-0.01550.011-0.005-0.0025-16.11420.18959.9095
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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