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- PDB-5zfh: Mouse Kallikrein 7 -

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Basic information

Entry
Database: PDB / ID: 5zfh
TitleMouse Kallikrein 7
ComponentsKallikrein-7
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / Degradation of the extracellular matrix / cornified envelope / serine-type endopeptidase activity / proteolysis / extracellular space
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 / Trypsin-like serine proteases ...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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSugawara, H.
Citation
Journal: Bioorg. Med. Chem. / Year: 2018
Title: Structure-based drug design to overcome species differences in kallikrein 7 inhibition of 1,3,6-trisubstituted 1,4-diazepan-7-ones.
Authors: Murafuji, H. / Sugawara, H. / Goto, M. / Oyama, Y. / Sakai, H. / Imajo, S. / Tomoo, T. / Muto, T.
#1: Journal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors.
Authors: Murafuji, H. / Sakai, H. / Goto, M. / Imajo, S. / Sugawara, H. / Muto, T.
History
DepositionMar 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-7


Theoretical massNumber of molelcules
Total (without water)24,6371
Polymers24,6371
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.795, 71.795, 100.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Kallikrein-7 / Serine protease 6 / Stratum corneum chymotryptic enzyme / Thymopsin


Mass: 24637.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klk7, Prss6, Scce / Production host: Escherichia coli (E. coli)
References: UniProt: Q91VE3, stratum corneum chymotryptic enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG8000, PEG400, magnesium chloride, Tris/HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→100 Å / Num. obs: 18987 / % possible obs: 93 % / Redundancy: 11.4 % / Net I/σ(I): 14
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y9L

5y9l


Resolution: 1.93→32.11 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.649 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23859 973 5.1 %RANDOM
Rwork0.18643 ---
obs0.18893 18001 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.592 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å20 Å2
2---5.27 Å20 Å2
3---10.54 Å2
Refinement stepCycle: 1 / Resolution: 1.93→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 0 131 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191761
X-RAY DIFFRACTIONr_bond_other_d0.0010.021613
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9582388
X-RAY DIFFRACTIONr_angle_other_deg0.733784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41625.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5915312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.181155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211917
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02316
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_it1.661.91895
X-RAY DIFFRACTIONr_mcbond_other1.6541.906894
X-RAY DIFFRACTIONr_mcangle_it2.4192.8561117
X-RAY DIFFRACTIONr_mcangle_other2.4192.861118
X-RAY DIFFRACTIONr_scbond_it2.6052.268866
X-RAY DIFFRACTIONr_scbond_other2.6042.268866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9823.2611271
X-RAY DIFFRACTIONr_long_range_B_refined5.19823.4951953
X-RAY DIFFRACTIONr_long_range_B_other5.17523.3051939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 63 -
Rwork0.322 1131 -
obs--82.23 %
Refinement TLS params.Method: refined / Origin x: -18.6632 Å / Origin y: 26.8403 Å / Origin z: 44.0264 Å
111213212223313233
T0.0549 Å2-0.0248 Å20.0246 Å2-0.0343 Å2-0.0185 Å2--0.0155 Å2
L0.843 °2-0.267 °2-0.3486 °2-1.5537 °2-0.0054 °2--1.1174 °2
S0.0225 Å °-0.0505 Å °0.0054 Å °0.0505 Å °-0.0798 Å °0.0417 Å °0.0547 Å °0.0163 Å °0.0573 Å °

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