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- PDB-1l2e: Human Kallikrein 6 (hK6) Active Form with benzamidine inhibitor -

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Basic information

Entry
Database: PDB / ID: 1l2e
TitleHuman Kallikrein 6 (hK6) Active Form with benzamidine inhibitor
ComponentsKallikrein 6
KeywordsHYDROLASE / serine protease / kallikrein / human kallikrein 6 / benzamidine / protease / myelencephalon specific protease / zyme / protease M / neurosin
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 / 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
BENZAMIDINE / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBernett, M.J. / Blaber, S.I. / Scarisbrick, I.A. / Blaber, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure and biochemical characterization of human kallikrein 6 reveals that a trypsin-like kallikrein is expressed in the central nervous system.
Authors: Bernett, M.J. / Blaber, S.I. / Scarisbrick, I.A. / Dhanarajan, P. / Thompson, S.M. / Blaber, M.
History
DepositionFeb 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE The residue numbering is not sequential.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6773
Polymers24,5331
Non-polymers1442
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.10, 62.08, 85.75
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 6 / HK6


Mass: 24532.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92876
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
240 mMsodium acetate1drop
3100 mM1dropNaCl
420 mMbenzamidine1droppH4.5
530 %(w/v)PEG40001reservoir
60.2 Mmagnesium chloride hexahydrate1reservoir
70.1 MTris-hydrochloride1reservoirpH8.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 24, 2001 / Details: Osmic Blue Confocal Mirrors
RadiationMonochromator: Osmic blue confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→43 Å / Num. all: 22918 / Num. obs: 21777 / % possible obs: 96 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 21.6 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 43
Reflection shellResolution: 1.75→1.79 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.9 / % possible all: 82.7
Reflection
*PLUS
Lowest resolution: 43 Å / Num. measured all: 495027
Reflection shell
*PLUS
% possible obs: 82.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0J

1a0j


Resolution: 1.75→43 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.241 581 3 %Random
Rwork0.209 ---
obs0.23 19044 87.6 %-
all-19625 --
Displacement parametersBiso mean: 26.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 10 139 1841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.75→1.86 Å
RfactorNum. reflection
Rfree0.296 87
Rwork0.287 -
obs-2442
Refinement
*PLUS
Lowest resolution: 43 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.287

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