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Yorodumi- PDB-1ciz: X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXES W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ciz | ||||||
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Title | X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXES WITH NON-PEPTIDE INHIBITORS: IMPLICATION FOR INHIBITOR SELECTIVITY | ||||||
Components | PROTEIN (STROMELYSIN-1) | ||||||
Keywords | METALLOPROTEINASE / MATRIX METALLOPROTEINASE / MMP-3 / NON-PEPTIDE INHIBITOR | ||||||
Function / homology | Function and homology information stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / EGFR Transactivation by Gastrin / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 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 | 1ciz.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ciz.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ciz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1ciz ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1ciz | HTTPS FTP |
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-Related structure data
Related structure data | 1b8ySC 1caqC 1qiaC 1qicC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 18887.029 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: FIBROBLAST / Plasmid: PGEMEX-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1 |
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-Non-polymers , 5 types, 154 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-DPS / | #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: 2.37 Å3/Da / Density % sol: 48.05 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 87 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: SUPPER 8CM/16CM FOCUSING MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→10 Å / Num. obs: 21098 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.038 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.64→1.7 Å / Mean I/σ(I) obs: 11.2 / Rsym value: 0.121 / % possible all: 92.4 |
Reflection | *PLUS Num. obs: 20986 / Num. measured all: 80181 / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 92.4 % / Rmerge(I) obs: 0.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROTEIN FROM 1B8Y Resolution: 1.64→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.64→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 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 Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.6 Å / Rfactor Rfree: 0.305 / % reflection Rfree: 11 % / Rfactor Rwork: 0.308 |