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Yorodumi- PDB-1jaq: COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jaq | ||||||
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Title | COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) | ||||||
Components | MATRIX METALLO PROTEINASE-8 (MET80 FORM) | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEASE / ZINC-ENDOPEPTIDASE / METZINCINS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 / Resolution: 2.4 Å | ||||||
Authors | Grams, F. / Reinemer, P. / Powers, J.C. / Kleine, T. / Piper, M. / Tschesche, H. / Huber, R. / Bode, W. | ||||||
Citation | 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. #1: Journal: Embo J. / Year: 1994 Title: The X-Ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited by a Substrate Analogue Reveals the Essentials for Catalysis and Specificity Authors: Bode, W. / Reinemer, P. / Huber, R. / Kleine, T. / Schnierer, S. / Tschesche, H. #2: Journal: FEBS Lett. / Year: 1994 Title: Structural Implications for the Role of the N Terminus in the 'Superactivation' of Collagenases. A Crystallographic Study Authors: Reinemer, P. / Grams, F. / Huber, R. / Kleine, T. / Schnierer, S. / Piper, M. / Tschesche, H. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jaq.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jaq.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1jaq ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1jaq | HTTPS FTP |
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-Related 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: CATALYTIC DOMAIN, RESIDUES 80 - 242 Source method: isolated from a genetically manipulated source Details: MMP-8 IS IDENTICAL TO THE HUMAN NEUTROPHIL COLLAGENASE Source: (gene. exp.) Homo sapiens (human) / Cell: NEUTROPHILS / Production host: Escherichia coli (E. coli) / References: UniProt: P22894, neutrophil collagenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-01S / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Rmerge(I) obs: 0.121 |
Reflection | *PLUS Highest resolution: 2.05 Å / Num. all: 33433 / Num. obs: 9501 / % possible obs: 86.2 % / Num. measured all: 34521 |
Reflection shell | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 2.1 Å / % possible obs: 75.7 % |
-Processing
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Refinement | Resolution: 2.4→8 Å /
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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