+Open data
-Basic information
Entry | Database: PDB / ID: 1lyw | ||||||
---|---|---|---|---|---|---|---|
Title | CATHEPSIN D AT PH 7.5 | ||||||
Components | (CATHEPSIN D) x 2 | ||||||
Keywords | ASPARTIC PROTEASE / HYDROLASE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information cathepsin D / aspartic-type peptidase activity / regulation of establishment of protein localization / insulin catabolic process / lipoprotein catabolic process / insulin receptor recycling / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Collagen degradation / autophagosome assembly / Metabolism of Angiotensinogen to Angiotensins ...cathepsin D / aspartic-type peptidase activity / regulation of establishment of protein localization / insulin catabolic process / lipoprotein catabolic process / insulin receptor recycling / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Collagen degradation / autophagosome assembly / Metabolism of Angiotensinogen to Angiotensins / Insulin receptor recycling / MHC class II antigen presentation / lysosomal lumen / endosome lumen / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / melanosome / tertiary granule lumen / peptidase activity / aspartic-type endopeptidase activity / collagen-containing extracellular matrix / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / endosome membrane / lysosome / membrane raft / positive regulation of apoptotic process / lysosomal membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lee, A.Y. / Gulnik, S.V. / Erickson, J.W. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Conformational switching in an aspartic proteinase. Authors: Lee, A.Y. / Gulnik, S.V. / Erickson, J.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Crystal Structures of Native and Inhibited Forms of Human Cathepsin D: Implications for Lysosomal Targeting and Drug Design Authors: Baldwin, E.T. / Bhat, T.N. / Gulnik, S. / Hosur, M.V. / Sowder II, R.C. / Cachau, R.E. / Collins, J. / Silva, A.M. / Erickson, J.W. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Human Liver Cathepsin D. Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of a Lysosomal Enzyme Authors: Gulnik, S. / Baldwin, E.T. / Tarasova, N. / Erickson, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lyw.cif.gz | 336.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lyw.ent.gz | 279.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1lyw ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1lyw | HTTPS FTP |
---|
-Related structure data
Related structure data | 1lyaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 10688.941 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / References: UniProt: P07339, cathepsin D #2: Protein | Mass: 26270.207 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / References: UniProt: P07339, cathepsin D #3: Chemical | ChemComp-EPE / #4: Water | ChemComp-HOH / | Compound details | CATHEPSIN D IS FOUND PREDOMINANTLY IN A TWO-CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. ...CATHEPSIN D IS FOUND PREDOMINAN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.24 Å3/Da / Density % sol: 65 % / Description: DATA WAS COLLECTED USING 1 DEGREE OSCILLATION | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 190 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 197513 / % possible obs: 73 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 6.95 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.37 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2 / Rsym value: 0.318 / % possible all: 41 |
Reflection | *PLUS Num. obs: 68982 / Num. measured all: 197513 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LYA Resolution: 2.5→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 Details: ALTHOUGH THERE ARE NO NON-CRYSTALLOGRAPHIC SYMMETRIC AXIES. WE DID NOT BOTHER TO LOCATE THEM. THEREFORE, NON-CRYSTALLOGRAPHIC SYMMETRY ARE NOT USED FOR OUR REFINEMENT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|