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- PDB-1sln: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STR... -
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Basic information
Entry | Database: PDB / ID: 1sln | |||||||||
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Title | CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-702,842 | |||||||||
![]() | STROMELYSIN-1 | |||||||||
![]() | HYDROLASE / METALLOPROTEASE / FIBROBLAST / COLLAGEN DEGRADATION | |||||||||
Function / homology | ![]() 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / 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 | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Becker, J.W. | |||||||||
![]() | ![]() Title: Stromelysin-1: three-dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme. Authors: Becker, J.W. / Marcy, A.I. / Rokosz, L.L. / Axel, M.G. / Burbaum, J.J. / Fitzgerald, P.M. / Cameron, P.M. / Esser, C.K. / Hagmann, W.K. / Hermes, J.D. / Springer, J.P. #1: ![]() Title: The NMR Structure of the Inhibited Catalytic Domain of Human Stromelysin-1 Authors: Gooley, P.R. / O'Connell, J.F. / Marcy, A.I. / Cuca, G.C. / Salowe, S.P. / Bush, B.L. / Hermes, J.D. / Esser, C.K. / Hagmann, W.K. / Springer, J.P. / Johnson, B.A. #2: ![]() Title: Inhibition of Matrix Metalloproteinases by N-Carboxyalkyl Peptides Authors: Chapman, K.T. / Kopka, I.E. / Durette, P.L. / Esser, C.K. / Lanza, T.J. / Izquierdo-Martin, M. / Niedzwiecki, L. / Chang, B. / Harrison, R.K. / Kuo, D.W. / Lin, T.-T. / Stein, R.L. / Hagmann, W.K. #3: ![]() Title: Human Fibroblast Stromelysin Catalytic Domain: Expression, Purification, and Characterization of a C-Terminally Truncated Form Authors: Marcy, A.I. / Eiberger, L.L. / Harrison, R. / Chan, H.K. / Hutchinson, N.I. / Hagmann, W.K. / Cameron, P.M. / Boulton, D.A. / Hermes, J.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.4 KB | Display | ![]() |
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PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743 KB | Display | ![]() |
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Full document | ![]() | 743.9 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19416.529 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 83 - 255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-8MI / | #5: Water | ChemComp-HOH / | Compound details | THERE IS A HYDROGEN BOND BETWEEN THE NITROGEN ATOM OF ALA 140 AND THE S-DELTA OF MET 143. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.54 Details: HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF ENZYME:INHIBITOR SOLUTION (9 MG/ML ENZYME, 1.5 MILLIMOLAR INHIBITOR, 5.0 MILLIMOLAR CALCIUM CHLORIDE, 0.02% SODIUM AZIDE, 20 MILLIMOLAR ...Details: HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF ENZYME:INHIBITOR SOLUTION (9 MG/ML ENZYME, 1.5 MILLIMOLAR INHIBITOR, 5.0 MILLIMOLAR CALCIUM CHLORIDE, 0.02% SODIUM AZIDE, 20 MILLIMOLAR TRIS HYDROCHLORIDE, PH 7.5) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (10% PEG-6000, 15% SATURATED AMMONIUM ACETATE 0.02% SODIUM AZIDE, 0.1 M CACODYLATE, PH 5.54) AND INCUBATED AT ROOM TEMPERATURE., vapor diffusion - hanging drop PH range: 5.54-7.5 / Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1990 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→8 Å / Num. obs: 8311 / % possible obs: 88.9 % / Observed criterion σ(I): 1 / Redundancy: 2.79 % / Biso Wilson estimate: 11.76 Å2 / Rmerge(I) obs: 0.0598 / Rsym value: 0.0758 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.26→2.41 Å / Redundancy: 1.71 % / Mean I/σ(I) obs: 4.03 / Rsym value: 0.189 / % possible all: 60.9 |
Reflection shell | *PLUS % possible obs: 60.9 % / Rmerge(I) obs: 0.189 |
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Processing
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Refinement | Resolution: 2.27→8 Å / Cross valid method: FREE-R / σ(F): 2
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Displacement parameters | Biso mean: 11.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.37 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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