+Open data
-Basic information
Entry | Database: PDB / ID: 1l2e | ||||||
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Title | Human Kallikrein 6 (hK6) Active Form with benzamidine inhibitor | ||||||
Components | Kallikrein 6 | ||||||
Keywords | HYDROLASE / serine protease / kallikrein / human kallikrein 6 / benzamidine / protease / myelencephalon specific protease / zyme / protease M / neurosin | ||||||
Function / homology | Function and homology information tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Bernett, M.J. / Blaber, S.I. / Scarisbrick, I.A. / Blaber, M. | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE The residue numbering is not sequential. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l2e.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l2e.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/1l2e ftp://data.pdbj.org/pub/pdb/validation_reports/l2/1l2e | HTTPS FTP |
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-Related structure data
Related structure data | 1a0jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-BEN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 24, 2001 / Details: Osmic Blue Confocal Mirrors |
Radiation | Monochromator: Osmic blue confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A0J Resolution: 1.75→43 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters | Biso mean: 26.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å
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Refinement | *PLUS Lowest resolution: 43 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.287 |