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- PDB-7qi0: Crystal structure of KLK6 in complex with compound DKFZ918 -

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Basic information

Entry
Database: PDB / ID: 7qi0
TitleCrystal structure of KLK6 in complex with compound DKFZ918
ComponentsKallikrein-6KLK6
KeywordsPEPTIDE BINDING PROTEIN / serine proteases
Function / homology
Function and homology information


tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / intercellular bridge / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / intercellular bridge / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-C9I / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsJagtap, P.K.A. / Baumann, A. / Lohbeck, J. / Isak, D. / Miller, A. / Hennig, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Adv / Year: 2022
Title: Scalable synthesis and structural characterization of reversible KLK6 inhibitors.
Authors: Baumann, A. / Isak, D. / Lohbeck, J. / Jagtap, P.K.A. / Hennig, J. / Miller, A.K.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-6
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6704
Polymers48,8352
Non-polymers8352
Water2,846158
1
A: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,4181
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,4181
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.410, 46.860, 68.230
Angle α, β, γ (deg.)90.000, 92.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-6 / KLK6 / Neurosin / Protease M / SP59 / Serine protease 18 / Serine protease 9 / Zyme


Mass: 24417.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Plasmid: pXLG / Production host: Homo sapiens (human) / Strain (production host): Expi293F
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-C9I / (5~{R})-3-(6-carbamimidoylpyridin-3-yl)-~{N}-[(1~{S})-1-naphthalen-1-ylpropyl]-2-oxidanylidene-1,3-oxazolidine-5-carboxamide


Mass: 417.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20 M trimethylamine N-oxide, 0.1 M Tris-HCl pH8.5, 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.88→37.46 Å / Num. obs: 32018 / % possible obs: 99 % / Redundancy: 6.498 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.119 / Χ2: 0.876 / Net I/σ(I): 9.07 / Num. measured all: 208040
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.935.2431.2540.8710952234220890.4261.39189.2
1.93-1.985.9591.0451.2313766231223100.6251.14899.9
1.98-2.046.4990.9191.5714694226222610.6561100
2.04-2.16.7120.6982.2814706219121910.8040.757100
2.1-2.176.6870.5712.8614157211821170.8590.62100
2.17-2.256.7680.4733.5913895205320530.8930.512100
2.25-2.336.8270.3944.3313558198719860.9270.42799.9
2.33-2.436.8730.3475.0113079190319030.9410.376100
2.43-2.546.7910.2885.9612359182218200.9590.31299.9
2.54-2.666.7710.2417.3611937176317630.9690.261100
2.66-2.86.7560.199.0111209165916590.9820.205100
2.8-2.976.6550.15510.8710675160516040.9850.16899.9
2.97-3.186.6010.12313.599736147814750.9920.13399.8
3.18-3.436.7030.09117.989351139613950.9940.09899.9
3.43-3.766.7050.0723.298549127812750.9970.07699.8
3.76-4.26.5760.05826.297622116211590.9970.06399.7
4.2-4.866.2960.05228.226554104210410.9980.05699.9
4.86-5.955.8460.05227.2550868708700.9970.057100
5.95-8.416.3330.04929.0543196876820.9980.05399.3
8.41-37.465.030.03630.6618364013650.9980.04191

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VFE

3vfe


Resolution: 1.88→37.46 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 1599 5 %
Rwork0.1904 --
obs0.1925 32008 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.97 Å2 / Biso mean: 50.2576 Å2 / Biso min: 22.29 Å2
Refinement stepCycle: final / Resolution: 1.88→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 62 158 3491
Biso mean--43.42 47.57 -
Num. residues----439
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)
13.9682-0.28420.76664.90921.03223.85550.13320.1712-0.17170.63850.2655-0.72330.69730.6965-0.21450.39150.1624-0.13350.3427-0.07430.336213.7849-4.44817.0348
25.67070.41091.02686.00661.26253.6083-0.13220.3440.61220.35430.2717-0.5465-0.11910.6116-0.10220.25780.0148-0.05950.3312-0.0090.323412.70018.39887.1457
34.77220.3943-0.67964.1066-0.9814.63230.0908-0.9865-0.17190.0402-0.0363-0.6106-0.40950.78850.02760.2917-0.10440.01220.46230.04080.317148.074214.010627.5643
45.38090.0576-0.93452.77540.21354.52920.0663-1.31550.48130.3077-0.0096-0.1211-0.74260.3563-0.13540.412-0.080500.5463-0.0820.289439.730218.2433.6222
56.56510.2974-0.79773.49960.23441.88770.2423-1.07010.65720.05870.0738-0.5065-1.1020.9779-0.1630.636-0.2750.0650.7344-0.14870.415648.647121.980629.9373
66.12551.0698-1.15332.36760.21563.69770.0395-0.25130.2205-0.17560.0808-0.0035-0.40330.1704-0.03850.3049-00.01680.2080.02440.248238.220815.094324.1342
77.41270.5975-0.0492.682-0.27044.5159-0.39240.5572-1.4316-0.36810.1533-0.37030.81880.61820.2760.4114-0.05450.14490.3297-0.01280.579744.36472.366215.8785
80.11030.4613-0.59444.4603-0.51037.27920.4199-2.057-1.10391.1191-0.0547-1.07870.22531.31580.78560.44510.0928-0.13211.42870.2930.701854.15167.408236.9555
92.99451.6627-1.0952.6944-0.54151.4838-1.0915-0.2644-3.0223-0.29570.4784-0.5930.80651.24210.41140.4850.04250.26950.02540.29641.187139.5075-5.241424.3115
103.1203-3.67431.56496.2044-1.22791.10610.0873-1.1165-1.22520.1323-0.4021-0.44540.59850.80880.20770.41770.13090.04760.79890.3970.743248.7994-1.082430.4089
114.17851.6545-1.07164.69520.61963.8413-0.2207-0.2282-0.8179-0.40030.0087-0.21930.1680.36220.10920.24860.00360.0780.26330.11850.362338.75825.438122.4167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 140 )A16 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 246 )A141 - 246
3X-RAY DIFFRACTION3chain 'B' and (resid 16 through 54 )B16 - 54
4X-RAY DIFFRACTION4chain 'B' and (resid 55 through 67 )B55 - 67
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 90 )B69 - 90
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 123 )B91 - 123
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 140 )B124 - 140
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 155 )B141 - 155
9X-RAY DIFFRACTION9chain 'B' and (resid 156 through 184 )B156 - 184
10X-RAY DIFFRACTION10chain 'B' and (resid 185 through 199 )B185 - 199
11X-RAY DIFFRACTION11chain 'B' and (resid 200 through 246 )B200 - 246

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