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Yorodumi- PDB-1qrp: Human pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qrp | ||||||
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Title | Human pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME | ||||||
Components | PEPSIN 3A | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEINASE / PHOSPHONATE INHIBITOR / TRANSITION STATE ANALOGUE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information multivesicular body lumen / pepsin A / Surfactant metabolism / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.96 Å | ||||||
Authors | Fujinaga, M. / Cherney, M.M. / Tarasova, N.I. / Bartlett, P.A. / Hanson, J.E. / James, M.N.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog. Authors: Fujinaga, M. / Cherney, M.M. / Tarasova, N.I. / Bartlett, P.A. / Hanson, J.E. / James, M.N. #1: Journal: Protein Sci. / Year: 1995 Title: Crystal structure of human pepsin and its complex with pepstatin Authors: Fujinaga, M. / Chernaia, M.M. / Tarasova, N.I. / Mosimann, S.C. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qrp.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qrp.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1qrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qrp_validation.pdf.gz | 711 KB | Display | wwPDB validaton report |
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Full document | 1qrp_full_validation.pdf.gz | 712.7 KB | Display | |
Data in XML | 1qrp_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1qrp_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qrp ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qrp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34631.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00790, UniProt: P0DJD7*PLUS |
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#2: Chemical | ChemComp-HH0 / |
#3: 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: 3.14 Å3/Da / Density % sol: 60.77 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 40% AMMONIUM SULFATE, 100MM SODIUM ACETATE, 5% MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Aug 29, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→65 Å / Num. all: 31990 / % possible obs: 89.3 % / Observed criterion σ(F): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.108 |
Reflection shell | Resolution: 1.96→2 Å / % possible all: 64.2 |
Reflection | *PLUS Num. obs: 31990 / Num. measured all: 188324 |
Reflection shell | *PLUS % possible obs: 64.2 % |
-Processing
Software |
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Refinement | Resolution: 1.96→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: GROMOS87 FORCE FIELD
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Refinement step | Cycle: LAST / Resolution: 1.96→30 Å
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Refine LS restraints |
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Software | *PLUS Name: GROMOS87 / Classification: refinement | ||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |