+Open data
-Basic information
Entry | Database: PDB / ID: 3hha | ||||||
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Title | Crystal structure of cathepsin L in complex with AZ12878478 | ||||||
Components | Cathepsin L1 | ||||||
Keywords | HYDROLASE / PROTEROS BIOSTRUCTURES GMBH / Cathepsin L / Inhibitors / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen | ||||||
Function / homology | Function and homology information enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / Collagen degradation / fibronectin binding / antigen processing and presentation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / positive regulation of apoptotic signaling pathway / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.27 Å | ||||||
Authors | Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. ...Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. / Karoutchi, G.I. / Kenny, P.W. / Morley, A.D. / Oldham, K. / Rankine, N. / Ryan, D. / Wells, S.L. / Wood, L. / Augustin, M. / Krapp, S. / Simader, H. / Steinbacher, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Dipeptidyl nitrile inhibitors of Cathepsin L. Authors: Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J.E. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. / Karoutchi, G.I. / Kenny, P.W. / Morley, A.D. / ...Authors: Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J.E. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. / Karoutchi, G.I. / Kenny, P.W. / Morley, A.D. / Oldham, K. / Rankine, N. / Ryan, D. / Wells, S.L. / Wood, L. / Augustin, M. / Krapp, S. / Simader, H. / Steinbacher, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hha.cif.gz | 389.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hha.ent.gz | 332.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/3hha ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hha | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24161.676 Da / Num. of mol.: 4 / Fragment: Heavy chain and light chain: UNP residues 76-333 / Mutation: T223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL1, CTSL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07711, cathepsin L |
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-Non-polymers , 6 types, 1001 molecules
#2: Chemical | ChemComp-NOW / #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE MUTATION LISTED IN SEQADV RECORDS HAS BEEN INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.4 / Details: PEG, pH 7.4, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2007 / Details: LN2 cooled fixed-exit |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→44.28 Å / Num. all: 182842 / Num. obs: 182842 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.034 |
Reflection shell | Resolution: 1.27→1.33 Å / Redundancy: 0.4 % / Rmerge(I) obs: 0.098 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.27→44.28 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.253 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.158 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→44.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.27→1.303 Å / Total num. of bins used: 20
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