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Yorodumi- PDB-1i76: COMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i76 | ||||||
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Title | COMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID (D-TIC DERIVATIVE) WITH T CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) | ||||||
Components | NEUTROPHIL COLLAGENASE | ||||||
Keywords | HYDROLASE / COMPLEX (METALLOPROTEASE-INHIBITOR) | ||||||
Function / homology | Function and homology information neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Gavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2000 Title: Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design. Authors: Gavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A. #1: Journal: J.Med.Chem. / Year: 1999 Title: QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP OF HUMAN NEUTROPHIL COLLAGENASE (MMP8-8) INHIBITORS USING COMPARATIVE MOLECULAR FIELD ANALYSIS AND X-RAY STRUCTURE ANALYSIS Authors: Matter, H. / Schwab, W. / Barbier, D. / Billen, G. / Haase, B. / Schudok, M. / Neises, B. / Thorwart, W. / Schreuder, H. / Brachvogel, V. / Weithmann, K.U. / Loenze, P. #2: Journal: Eur.J.Biochem. / Year: 1995 Title: X-RAY STRUCTURES OF HUMAN NEUTROPHIL COLLAGENASE COMPLEXED WITH PEPTIDE HYDROXAMATE AND PEPTIDE THIOL INHIBITORS. IMPLICATIONS FOR SUBSTRATE BINDING AND RATIONAL DRUG DESIGN Authors: Grams, F. / Reinemer, P. / Powers, J.C. / Kleine, T. / Pieper, M. / Tschesche, H. / Huber, R. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i76.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i76.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1i76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i76_validation.pdf.gz | 728 KB | Display | wwPDB validaton report |
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Full document | 1i76_full_validation.pdf.gz | 731.1 KB | Display | |
Data in XML | 1i76_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1i76_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i76 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i76 | HTTPS FTP |
-Related structure data
Related structure data | 1i73C 1japS 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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Unit cell |
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-Components
#1: Protein | Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: RESIDUES 80-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22894, neutrophil collagenase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-BSI / | #5: 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: 2.21 Å3/Da / Density % sol: 44.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES-NAOH, NaCl, CaCl2, ZnCl2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃Details: 2 micro litte of protein solution, 1 miro litter of inhibitor solution, and 5 micro litter of PEG solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 21, 1998 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 51100 / Num. obs: 50709 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5 / % possible all: 95.3 |
Reflection | *PLUS Num. measured all: 411807 |
Reflection shell | *PLUS % possible obs: 95.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JAP Resolution: 1.2→10 Å / Num. parameters: 14352 / Num. restraintsaints: 17304 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 1201 / Occupancy sum non hydrogen: 1586 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→10 Å
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