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- PDB-5fah: KALLIKREIN-7 IN COMPLEX WITH COMPOUND1 -

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Basic information

Entry
Database: PDB / ID: 5fah
TitleKALLIKREIN-7 IN COMPLEX WITH COMPOUND1
ComponentsKallikrein-7
KeywordsHYDROLASE
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / metalloendopeptidase activity ...stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / metalloendopeptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
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 / Trypsin-like serine proteases ...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 / 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
Chem-5VT / ACETATE ION / Kallikrein-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsOstermann, N. / Zink, F.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Small-molecule factor D inhibitors targeting the alternative complement pathway.
Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. ...Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. / Dussauge, S. / Hughes, N. / Delgado, O. / Hommel, U. / Gould, T. / Mac Sweeney, A. / Gerhartz, B. / Cumin, F. / Flohr, S. / Schubart, A. / Jaffee, B. / Harrison, R. / Risitano, A.M. / Eder, J. / Anderson, K.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9663
Polymers24,4751
Non-polymers4912
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-1 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.611, 60.343, 80.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kallikrein-7 / / hK7 / Serine protease 6 / Stratum corneum chymotryptic enzyme / hSCCE


Mass: 24475.180 Da / Num. of mol.: 1 / Fragment: UNP residues 30-253 / Mutation: Tyr172Arg
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK7, PRSS6, SCCE / Production host: Escherichia coli (E. coli)
References: UniProt: P49862, stratum corneum chymotryptic enzyme
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-5VT / (2~{S})-~{N}2-[2-(4-methoxyphenyl)ethyl]-~{N}1-(naphthalen-1-ylmethyl)pyrrolidine-1,2-dicarboxamide


Mass: 431.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 microlitre Protein solution were mixed with 0.5 microlitre RESERVOIR solution. PROTEIN SOLUTION: 24.6 MG/ML KALLIKREIN 7, 50 MM SODIUM ACETATE PH 5.6, 100 MM NACL, 2 MM INHIBITOR, 1.8% ...Details: 0.5 microlitre Protein solution were mixed with 0.5 microlitre RESERVOIR solution. PROTEIN SOLUTION: 24.6 MG/ML KALLIKREIN 7, 50 MM SODIUM ACETATE PH 5.6, 100 MM NACL, 2 MM INHIBITOR, 1.8% DMSO, RESERVOIR SOLUTION: 35% PEG 3350, 100 MM SODIUM ACETATE PH 4.8, 200 MM CALCIUM CHLORIDE. CRYO: FLASH FREEZING IN LIQUID NITROGEN WITHOUT ADDITIONAL CRYO SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97991 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97991 Å / Relative weight: 1
ReflectionResolution: 1.1→29.29 Å / Num. obs: 65233 / % possible obs: 96 % / Redundancy: 3.8 % / Biso Wilson estimate: 11.95 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 34.7
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.2 / % possible all: 73.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
BUSTER2.11.5refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPJ

1spj


Resolution: 1.1→29.29 Å / Cor.coef. Fo:Fc: 0.9462 / Cor.coef. Fo:Fc free: 0.9485 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.043 / SU Rfree Cruickshank DPI: 0.041
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 6643 10.18 %RANDOM
Rwork0.1875 ---
obs0.1884 65233 99.25 %-
Displacement parametersBiso mean: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.6265 Å20 Å20 Å2
2--0.9588 Å20 Å2
3----0.3323 Å2
Refine analyzeLuzzati coordinate error obs: 0.139 Å
Refinement stepCycle: LAST / Resolution: 1.1→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 36 223 1989
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011820HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112488HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d628SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes273HARMONIC5
X-RAY DIFFRACTIONt_it1820HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.13
X-RAY DIFFRACTIONt_other_torsion13.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion233SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2316SEMIHARMONIC4
LS refinement shellResolution: 1.1→1.23 Å
RfactorNum. reflection% reflection
Rfree0.1949 480 10.05 %
Rwork0.1747 4298 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: 12.1833 Å / Origin y: 3.7756 Å / Origin z: 33.8441 Å
111213212223313233
T-0.0235 Å2-0.0008 Å20.002 Å2--0.028 Å2-0.0087 Å2---0.0257 Å2
L0.6637 °20.0258 °20.1169 °2-0.5562 °2-0.1303 °2--0.6365 °2
S0.0071 Å °0.0361 Å °-0.0452 Å °-0.0361 Å °0.008 Å °0.0148 Å °0.0299 Å °0.0216 Å °-0.0151 Å °
Refinement TLS groupSelection details: { A|* }

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