+Open data
-Basic information
Entry | Database: PDB / ID: 1bzs | ||||||
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Title | CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909 | ||||||
Components | NEUTROPHIL COLLAGENASE | ||||||
Keywords | HYDROLASE / METALLO PROTEINASE / HYDROXAMATE / MATRIX 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Schreuder, H. / Brachvogel, V. / Loenze, P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1999 Title: Quantitative structure-activity relationship of human neutrophil collagenase (MMP-8) inhibitors using comparative molecular field analysis and X-ray structure analysis. Authors: Matter, H. / Schwab, W. / Barbier, D. / Billen, G. / Haase, B. / Neises, B. / Schudok, M. / Thorwart, W. / Schreuder, H. / Brachvogel, V. / Lonze, P. / Weithmann, K.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bzs.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bzs.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bzs_validation.pdf.gz | 710.2 KB | Display | wwPDB validaton report |
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Full document | 1bzs_full_validation.pdf.gz | 711.1 KB | Display | |
Data in XML | 1bzs_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1bzs_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bzs ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bzs | HTTPS FTP |
-Related structure data
Related structure data | 1janS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18374.008 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: NEUTROPHIL / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): BL21 / References: UniProt: P22894, neutrophil collagenase |
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-Non-polymers , 5 types, 214 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-BSI / | #5: Chemical | ChemComp-EPE / | #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: 2.16 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PROTEIN SOLUTION: 10 MG/ML MMP8 IN 25 MM MES, 100 MM NACL, 20 MM CACL2, 0.1 MM ZNCL2, PH 6.0, WITH THREEFOLD EXCESS INHIBITOR IN DMF ADDED. RESERVOIR SOLUTION: 10-25% (W/W) PEG6000. CRYSTALS ...Details: PROTEIN SOLUTION: 10 MG/ML MMP8 IN 25 MM MES, 100 MM NACL, 20 MM CACL2, 0.1 MM ZNCL2, PH 6.0, WITH THREEFOLD EXCESS INHIBITOR IN DMF ADDED. RESERVOIR SOLUTION: 10-25% (W/W) PEG6000. CRYSTALS APPEAR IN ABOUT 1 WEEK., VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 29, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 18344 / % possible obs: 99.8 % / Redundancy: 7 % / Rsym value: 4.8 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.7→2 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 17.2 / Rsym value: 9.6 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 129143 / Rmerge(I) obs: 0.048 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JAN Resolution: 1.7→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 0
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Displacement parameters | Biso mean: 13.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Rfactor Rwork: 0.273 |