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Yorodumi- PDB-1mmb: COMPLEX OF BB94 WITH THE CATALYTIC DOMAIN OF MATRIX METALLOPROTEI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mmb | ||||||
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Title | COMPLEX OF BB94 WITH THE CATALYTIC DOMAIN OF MATRIX METALLOPROTEINASE-8 | ||||||
Components | MATRIX METALLOPROTEINASE-8 | ||||||
Keywords | HYDROLASE (METALLOPROTEASE) / HYDROLASE / METALLOPROTEASE / METZINCINS / COLLAGEN DEGRADATION | ||||||
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 / collagen-containing extracellular matrix / endopeptidase activity / cellular response to lipopolysaccharide / 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: 2.1 Å | ||||||
Authors | Bode, W. / Grams, F. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor. Authors: Grams, F. / Crimmin, M. / Hinnes, L. / Huxley, P. / Pieper, M. / Tschesche, H. / Bode, W. #1: 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. #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. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mmb.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mmb.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 1mmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmb ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Details: MMP-8 IS IDENTICAL TO THE HUMAN NEUTROPHIL, COLLAGENASE Source: (gene. exp.) Homo sapiens (human) / Organ: NEUTROPHILS / Production host: Escherichia coli (E. coli) / References: UniProt: P22894, neutrophil collagenase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-BAT / | #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 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 | Num. obs: 9465 / % possible obs: 89.1 % / Rmerge(I) obs: 0.103 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 9999 Å / Num. all: 32085 / Num. measured all: 33465 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / % possible obs: 34.8 % |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å /
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.189 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / Rfactor obs: 0.295 |