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- PDB-7qft: Crystal structure of KLK6 in complex with compound 16a -

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Basic information

Entry
Database: PDB / ID: 7qft
TitleCrystal structure of KLK6 in complex with compound 16a
Components
  • KLK6 Activity-Based Probe (Ahx-DPhe-Cha-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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 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 1.0Nov 9, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id
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 / Refinement description / 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_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
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_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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-Cha-Dht-Arg-DPP)
D: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)50,7664
Polymers50,7664
Non-polymers00
Water7,927440
1
A: Kallikrein-6
D: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)25,3832
Polymers25,3832
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-6
C: KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Theoretical massNumber of molelcules
Total (without water)25,3832
Polymers25,3832
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.370, 39.970, 65.070
Angle α, β, γ (deg.)81.900, 84.950, 70.710
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 25 or resid 27...
d_2ens_1(chain "B" and (resid 16 through 25 or resid 27...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUTHRTHRAA16 - 251 - 10
d_12HISHISSERSERAA27 - 8312 - 66
d_13VALVALALAALAAA85 - 24468 - 222
d_14DPNDPNA1H2EA1H2EDD1 - 42 - 5
d_21LEULEUTHRTHRBB16 - 251 - 10
d_22HISHISSERSERBB27 - 8312 - 66
d_23VALVALALAALABB85 - 24468 - 222
d_24ACAACAA1H2EA1H2ECC1 - 51 - 5

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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) / Strain (production host): Expi293F
References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide KLK6 Activity-Based Probe (Ahx-DPhe-Cha-Dht-Arg-DPP)


Mass: 965.150 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.: 440 / 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: 1.91 Å3/Da / Density % sol: 35.52 %
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: 1.47→64.36 Å / Num. obs: 57658 / % possible obs: 94.7 % / Redundancy: 3.407 % / Biso Wilson estimate: 16.13 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.097 / Χ2: 0.903 / Net I/σ(I): 9.2 / Num. measured all: 196458 / Scaling rejects: 132
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
1.47-1.513.1731.2141.311333448135720.361.45179.7
1.51-1.553.4470.8841.9214302440341490.5621.04694.2
1.55-1.63.4660.6442.5114159432140850.6890.76294.5
1.6-1.653.4730.4723.3313415406538630.790.55895
1.65-1.73.450.3683.9413144401838100.860.43594.8
1.7-1.763.3620.2824.8312593392137460.9180.33495.5
1.76-1.833.1010.2185.7211194376736100.9350.26495.8
1.83-1.93.1790.1717.0410893360134270.9610.20795.2
1.9-1.993.4110.1289.3111311347533160.9760.15395.4
1.99-2.083.570.10411.1511270328531570.9830.12296.1
2.08-2.23.6140.08912.6911043315130560.9880.10597
2.2-2.333.50.08413.7110090298028830.9890.09996.7
2.33-2.493.5370.07514.589662281027320.990.08997.2
2.49-2.693.4510.06915.538715260425250.990.08297
2.69-2.953.3810.06316.777895239423350.9920.07597.5
2.95-3.33.1070.05417.866437215220720.9920.06696.3
3.3-3.813.2180.05119.975902193518340.9930.06294.8
3.81-4.663.7310.0522.975839159215650.9950.05998.3
4.66-6.593.8140.0523.234771126412510.9870.05899
6.59-64.363.7160.04523.624906766700.9950.05399.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3vfe


Resolution: 1.47→64.36 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.3781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2042 2881 5 %
Rwork0.1719 54762 -
obs0.1735 57643 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.47→64.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 109 440 3914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743582
X-RAY DIFFRACTIONf_angle_d1.2374875
X-RAY DIFFRACTIONf_chiral_restr0.102530
X-RAY DIFFRACTIONf_plane_restr0.0083632
X-RAY DIFFRACTIONf_dihedral_angle_d13.7667613
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.20597819608 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.51191010.43161942X-RAY DIFFRACTION71.94
1.5-1.520.38331380.30282608X-RAY DIFFRACTION93.34
1.52-1.550.28931360.26752593X-RAY DIFFRACTION94.33
1.55-1.580.27451360.24312572X-RAY DIFFRACTION94.42
1.58-1.610.24491390.2352649X-RAY DIFFRACTION95.15
1.61-1.650.24981360.23272585X-RAY DIFFRACTION94.54
1.65-1.690.29411400.22082656X-RAY DIFFRACTION95.23
1.69-1.730.25661380.21022618X-RAY DIFFRACTION95.13
1.73-1.780.21791370.18852607X-RAY DIFFRACTION95.61
1.78-1.830.22121400.17612672X-RAY DIFFRACTION95.91
1.83-1.890.20191380.17992607X-RAY DIFFRACTION95.05
1.89-1.960.21231370.17012602X-RAY DIFFRACTION94.97
1.96-2.030.22111410.16452677X-RAY DIFFRACTION96.54
2.03-2.130.21271400.16442662X-RAY DIFFRACTION96.12
2.13-2.240.2221390.16182656X-RAY DIFFRACTION96.81
2.24-2.380.20231420.16272695X-RAY DIFFRACTION97.12
2.38-2.560.23861400.16622654X-RAY DIFFRACTION97.12
2.56-2.820.17841400.16782683X-RAY DIFFRACTION97.28
2.82-3.230.16861410.16112675X-RAY DIFFRACTION97
3.23-4.070.15761380.13592626X-RAY DIFFRACTION95.47
4.07-64.360.16621440.15262723X-RAY DIFFRACTION98.83

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