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- PDB-6kbr: Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor... -

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Basic information

Entry
Database: PDB / ID: 6kbr
TitleCrystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex
Components
  • K41043
  • Kallikrein-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein engineering / Cystine knot protein / Protease inhibitor / Structural analysis / PROTEIN BINDING / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


biomineral tissue development / acrosome assembly / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / spermatid development / serine-type peptidase activity / acrosomal vesicle / secretory granule ...biomineral tissue development / acrosome assembly / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / spermatid development / serine-type peptidase activity / acrosomal vesicle / secretory granule / protein maturation / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Serine protease inhibitor Kazal-type 2 / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site ...Serine protease inhibitor Kazal-type 2 / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease inhibitor Kazal-type 2 / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKawaguchi, Y. / Nishimiya, D.
CitationJournal: Sci Rep / Year: 2019
Title: A protein scaffold, engineered SPINK2, for generation of inhibitors with high affinity and specificity against target proteases.
Authors: Nishimiya, D. / Kawaguchi, Y. / Kodama, S. / Nasu, H. / Yano, H. / Yamaguchi, A. / Tamura, M. / Hashimoto, R.
History
DepositionJun 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 22, 2023Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-4
C: K41043
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4003
Polymers34,3082
Non-polymers921
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-10 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.208, 41.620, 43.590
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Kallikrein-4 / Enamel matrix serine proteinase 1 / Kallikrein-like protein 1 / KLK-L1 / Prostase / Serine protease 17


Mass: 27048.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Production host: Homo sapiens (human)
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein K41043 / SPINK2


Mass: 7259.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Origami vector p7308 (others) / References: UniProt: P20155*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 35.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Lithium chloride, polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→72.577 Å / Num. obs: 20687 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.245 / Num. unique obs: 1283

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDG

2bdg


Resolution: 2→72.577 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.053 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22584 897 5 %RANDOM
Rwork0.18541 ---
obs0.18747 16901 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.645 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→72.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 6 110 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192137
X-RAY DIFFRACTIONr_bond_other_d0.0020.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9522904
X-RAY DIFFRACTIONr_angle_other_deg1.09234533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47725.05787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18115339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.053158
X-RAY DIFFRACTIONr_chiral_restr0.120.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212445
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02469
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0550.9521110
X-RAY DIFFRACTIONr_mcbond_other1.0540.9481109
X-RAY DIFFRACTIONr_mcangle_it1.7311.4141384
X-RAY DIFFRACTIONr_mcangle_other1.731.4181385
X-RAY DIFFRACTIONr_scbond_it1.7051.1511027
X-RAY DIFFRACTIONr_scbond_other1.7051.1511027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7041.6461521
X-RAY DIFFRACTIONr_long_range_B_refined3.9087.812415
X-RAY DIFFRACTIONr_long_range_B_other3.9077.8122416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 72 -
Rwork0.185 1211 -
obs--99.77 %

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