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- PDB-7qfv: Crystal structure of KLK6 in complex with compound 17a -

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Basic information

Entry
Database: PDB / ID: 7qfv
TitleCrystal structure of KLK6 in complex with compound 17a
Components
  • KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)
  • Kallikrein-6
KeywordsPEPTIDE BINDING PROTEIN / serine proteases
Function / homology
Function and homology information


tissue regeneration / cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / intercellular bridge / myelination / protein maturation / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
polypeptide(D) / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsJagtap, P.K.A. / Zhang, L. / De Vita, E. / Tate, E.W. / Hennig, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: A KLK6 Activity-Based Probe Reveals a Role for KLK6 Activity in Pancreatic Cancer Cell Invasion.
Authors: Zhang, L. / Lovell, S. / De Vita, E. / Jagtap, P.K.A. / Lucy, D. / Goya Grocin, A. / Kjaer, S. / Borg, A. / Hennig, J. / Miller, A.K. / Tate, E.W.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jan 31, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2

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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
C: KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)
D: KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)50,8144
Polymers50,8144
Non-polymers00
Water6,557364
1
A: Kallikrein-6
C: KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)25,4072
Polymers25,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
D: KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)25,4072
Polymers25,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.430, 40.080, 65.210
Angle α, β, γ (deg.)82.080, 84.950, 70.870
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Kallikrein-6 / 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) / Variant (production host): Expi293F
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Polypeptide(D) KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)


Mass: 989.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 1.92 Å3/Da / Density % sol: 36.02 %
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: ID30B / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.56→64.52 Å / Num. obs: 49476 / % possible obs: 94.8 % / Redundancy: 3.442 % / Biso Wilson estimate: 18.3 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.117 / Χ2: 0.872 / Net I/σ(I): 7.75 / Num. measured all: 170314 / Scaling rejects: 115
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
1.56-1.63.3681.2131.0610095385829970.3431.43777.7
1.6-1.643.5920.9061.5812622371835140.5211.06694.5
1.64-1.693.5770.716212652371535370.6620.84395.2
1.69-1.743.5360.5362.612031355634020.7750.63295.7
1.74-1.83.5140.43.3411392338932420.8630.47295.7
1.8-1.863.4460.3064.211059334732090.9030.36395.9
1.86-1.933.2070.2535.269758324430430.9240.30593.8
1.93-2.013.0560.1756.39058310829640.9520.21395.4
2.01-2.13.2010.1537.578920293827870.9620.18494.9
2.1-2.23.6310.1199.319986283127500.9810.13997.1
2.2-2.323.5040.11210.389139271426080.9790.13396.1
2.32-2.463.6170.09211.428969254024800.9870.10897.6
2.46-2.633.5730.08512.338404240323520.9870.197.9
2.63-2.843.4560.08213.067604224922000.9870.09697.8
2.84-3.113.4460.07114.56936205320130.9890.08498.1
3.11-3.483.1930.06515.545764184018050.9880.07998.1
3.48-4.023.0410.06216.154795165715770.990.07695.2
4.02-4.923.6880.06118.995012137313590.9910.07199
4.92-6.963.7850.06419.013997106010560.9920.07499.6
6.96-64.523.6510.05919.4721215895810.9910.06998.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VFE

3vfe


Resolution: 1.56→64.52 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 2470 5 %
Rwork0.1761 46943 -
obs0.1778 49413 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.55 Å2 / Biso mean: 22.8981 Å2 / Biso min: 9.66 Å2
Refinement stepCycle: final / Resolution: 1.56→64.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 118 364 3842
Biso mean--35.05 32.27 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.590.34541270.30532411253888
1.59-1.620.32921370.27762589272695
1.62-1.660.45531370.32332610274795
1.66-1.70.34171340.30462542267695
1.7-1.740.31361380.26052628276696
1.74-1.790.28231360.22082579271596
1.79-1.840.24451380.1992633277196
1.84-1.90.23011370.19772602273995
1.9-1.970.27451340.21872527266194
1.97-2.050.21171370.18942616275396
2.05-2.140.21151370.16142607274495
2.14-2.250.19671370.16722633277096
2.25-2.390.21941410.16632670281197
2.39-2.580.19721380.16832632277098
2.58-2.840.21571400.16542661280198
2.84-3.250.17461420.1612695283798
3.25-4.090.17691370.13632608274596
4.09-64.520.15761430.14942700284399

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