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Yorodumi- PDB-1b8y: X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b8y | ||||||
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Title | X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXED WITH NON-PEPTIDE INHIBITORS: IMPLICATIONS FOR INHIBITOR SELECTIVITY | ||||||
Components | PROTEIN (STROMELYSIN-1) | ||||||
Keywords | HYDROLASE / MATRIX METALLOPROTEINASE-3 / STROMELYSIN-1 | ||||||
Function / homology | Function and homology information stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / cellular response to nitric oxide / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / collagen catabolic process ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / cellular response to nitric oxide / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / collagen catabolic process / EGFR Transactivation by Gastrin / negative regulation of reactive oxygen species metabolic process / extracellular matrix disassembly / regulation of cell migration / Degradation of the extracellular matrix / extracellular matrix / cellular response to amino acid stimulus / extracellular matrix organization / cellular response to reactive oxygen species / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / endopeptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pavlovsky, A.G. / Williams, M.G. / Ye, Q.-Z. / Ortwine, D.F. / Purchase II, C.F. / White, A.D. / Dhanaraj, V. / Roth, B.D. / Johnson, L.L. / Hupe, D. ...Pavlovsky, A.G. / Williams, M.G. / Ye, Q.-Z. / Ortwine, D.F. / Purchase II, C.F. / White, A.D. / Dhanaraj, V. / Roth, B.D. / Johnson, L.L. / Hupe, D. / Humblet, C. / Blundell, T.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: implications for inhibitor selectivity. Authors: Pavlovsky, A.G. / Williams, M.G. / Ye, Q.Z. / Ortwine, D.F. / Purchase II, C.F. / White, A.D. / Dhanaraj, V. / Roth, B.D. / Johnson, L.L. / Hupe, D. / Humblet, C. / Blundell, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b8y.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8y.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8y_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 1b8y_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 1b8y_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1b8y_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8y ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18789.914 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1 |
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-Non-polymers , 5 types, 93 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-IN7 / [ | #6: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 51.35 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1995 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→29 Å / Num. obs: 13572 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Rsym value: 0.091 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 9.1 % / Rsym value: 0.345 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 142019 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: SIDE CHAINS OF RESIDUES PHE 154, GLU 216 AND ARG 233 ARE DISORDERED. TO REFLECT THIS, THEIR SIDE CHAIN ATOM OCCUPANCIES ARE SET TO ZERO. THE C TERMINAL PRO 250 IS NOT INCLUDED IN THE MODEL ...Details: SIDE CHAINS OF RESIDUES PHE 154, GLU 216 AND ARG 233 ARE DISORDERED. TO REFLECT THIS, THEIR SIDE CHAIN ATOM OCCUPANCIES ARE SET TO ZERO. THE C TERMINAL PRO 250 IS NOT INCLUDED IN THE MODEL BECAUSE OF THE LACK OF ELECTRON DENSITY CORRESPONDING TO THIS RESIDUE.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.249 / % reflection Rfree: 13 % / Rfactor Rwork: 0.215 |