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- PDB-5ms4: Kallikrein-related peptidase 8 leupeptin inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5ms4
TitleKallikrein-related peptidase 8 leupeptin inhibitor complex
Components
  • Kallikrein-8
  • LEUPEPTIN
KeywordsHydrolase/Inhibitor / trypsin-like serine protease / aldehyde inhibitor / Ca2+ complex / synaptic remodeling / Hydrolase-inhibitor complex
Function / homology
Function and homology information


kallikrein 8 / Formation of the cornified envelope / regulation of synapse organization / keratinocyte proliferation / serine protease inhibitor complex / neuron projection morphogenesis / memory / response to wounding / serine-type endopeptidase activity / proteolysis ...kallikrein 8 / Formation of the cornified envelope / regulation of synapse organization / keratinocyte proliferation / serine protease inhibitor complex / neuron projection morphogenesis / memory / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytoplasm
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
LEUPEPTIN / TERTIARY-BUTYL ALCOHOL / Kallikrein-8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsDebela, M. / Magdolen, V. / Skala, W. / Bode, W. / Brandstetter, H. / Goettig, P.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP25003-B21 Austria
CitationJournal: Sci Rep / Year: 2018
Title: Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin.
Authors: Debela, M. / Magdolen, V. / Skala, W. / Elsasser, B. / Schneider, E.L. / Craik, C.S. / Biniossek, M.L. / Schilling, O. / Bode, W. / Brandstetter, H. / Goettig, P.
History
DepositionDec 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 2.0Sep 18, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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
Revision 2.1Oct 9, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-8
B: Kallikrein-8
C: Kallikrein-8
D: Kallikrein-8
E: LEUPEPTIN
F: LEUPEPTIN
G: LEUPEPTIN
H: LEUPEPTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,03915
Polymers99,6578
Non-polymers3837
Water20,4831137
1
A: Kallikrein-8
E: LEUPEPTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1776
Polymers24,9142
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-8
F: LEUPEPTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9543
Polymers24,9142
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-8
G: LEUPEPTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9543
Polymers24,9142
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kallikrein-8
H: LEUPEPTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9543
Polymers24,9142
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.103, 46.045, 103.349
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Kallikrein-8 / hK8 / Neuropsin / NP / Ovasin / Serine protease 19 / Serine protease TADG-14 / Tumor-associated ...hK8 / Neuropsin / NP / Ovasin / Serine protease 19 / Serine protease TADG-14 / Tumor-associated differentially expressed gene 14 protein


Mass: 24484.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK8, NRPN, PRSS19, TADG14, UNQ283/PRO322 / Production host: Escherichia coli (E. coli) / References: UniProt: O60259, kallikrein 8
#2: Protein/peptide
LEUPEPTIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: LEUPEPTIN
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1137 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 35% (v/v) tert-Butanol, 0.1 M tri-Na citrate/citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2008 / Details: Mirrors
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.72
ReflectionResolution: 2.1→103.318 Å / Num. obs: 45164 / % possible obs: 97.7 % / Redundancy: 3.4 % / Rsym value: 0.178 / Net I/σ(I): 6.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.8 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å65.53 Å
Translation2.5 Å65.53 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→65.53 Å / Cross valid method: FREE R-VALUE / σ(F): 2.38 / Phase error: 28.91
RfactorNum. reflection% reflection
Rfree0.259 2354 5.21 %
Rwork0.212 --
obs0.239 45152 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6844 0 134 1137 8115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047164
X-RAY DIFFRACTIONf_angle_d0.7719746
X-RAY DIFFRACTIONf_dihedral_angle_d15.4812696
X-RAY DIFFRACTIONf_chiral_restr0.0481043
X-RAY DIFFRACTIONf_plane_restr0.0051284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.14580.27011220.26512486X-RAY DIFFRACTION88
2.1458-2.19570.34031450.26742564X-RAY DIFFRACTION88
2.1957-2.25060.31481490.26152516X-RAY DIFFRACTION88
2.2506-2.31140.26591300.26252600X-RAY DIFFRACTION90
2.3114-2.37940.32171440.2582575X-RAY DIFFRACTION91
2.3794-2.45610.31421460.24472639X-RAY DIFFRACTION92
2.4561-2.54380.32241470.25262661X-RAY DIFFRACTION93
2.5438-2.64560.31451340.25172698X-RAY DIFFRACTION94
2.6456-2.76590.29861690.24742698X-RAY DIFFRACTION94
2.7659-2.91160.29251300.24952723X-RAY DIFFRACTION95
2.9116-3.09370.29061450.23642743X-RAY DIFFRACTION95
3.0937-3.33220.27751580.22762738X-RAY DIFFRACTION95
3.3322-3.66680.26051250.22042766X-RAY DIFFRACTION96
3.6668-4.19570.25721500.21172774X-RAY DIFFRACTION95
4.1957-5.27950.26031310.20212780X-RAY DIFFRACTION95
5.2795-26.91590.28061620.24042873X-RAY DIFFRACTION95

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