+Open data
-Basic information
Entry | Database: PDB / ID: 1cs8 | ||||||
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Title | CRYSTAL STRUCTURE OF PROCATHEPSIN L | ||||||
Components | HUMAN PROCATHEPSIN L | ||||||
Keywords | HYDROLASE / PROSEGMENT / PROPEPTIDE / INHIBITION | ||||||
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 / serpin family protein binding / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen ...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 / serpin family protein binding / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / fibronectin binding / protein autoprocessing / Collagen degradation / collagen catabolic process / cysteine-type peptidase activity / Attachment and Entry / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / lysosome / apical plasma membrane / symbiont entry into host cell / immune response / 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 / Resolution: 1.8 Å | ||||||
Authors | Cygler, M. / Coulombe, R. | ||||||
Citation | Journal: EMBO J. / Year: 1996 Title: Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment. Authors: Coulombe, R. / Grochulski, P. / Sivaraman, J. / Menard, R. / Mort, J.S. / Cygler, M. #1: Journal: Proteins / Year: 1998 Title: Structural Basis for Specificity of Papain-Like Cysteine Protease Proregions Toward Their Cognate Enzymes Authors: Groves, M.R. / Coulombe, R. / Jenkins, J. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cs8.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cs8.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cs8_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 1cs8_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 1cs8_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1cs8_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/1cs8 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/1cs8 | HTTPS FTP |
-Related 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: 35920.973 Da / Num. of mol.: 1 / Mutation: T110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P07711, cathepsin L |
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#2: 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: 3.76 Å3/Da / Density % sol: 67.26 % |
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Crystal grow | Temperature: 293.2 K / Method: microbatch / pH: 7.8 Details: Na,K,Phosphate, pH 7.8, MICROBATCH, temperature 20.2K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.924 |
Detector | Type: ADSC / Detector: CCD / Date: Feb 13, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.924 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45 Å / Num. all: 151997 / Num. obs: 47257 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.224 / Num. unique all: 3322 / % possible all: 66.7 |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Some residues have alternate conformations: G24P, M25P, N26P, E28P, Q73P, N108, K120, I132, S158, M201, H208. Several side-chains have occupancies set to zero or 0.5
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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