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Open data
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Basic information
Entry | Database: PDB / ID: 1kbc | ||||||
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Title | PROCARBOXYPEPTIDASE TERNARY COMPLEX | ||||||
![]() | NEUTROPHIL COLLAGENASE | ||||||
![]() | METALLOPROTEINASE / HYDROLYTIC ENZYME / COLLAGENASE / MATRIXIN / MMP-8 / HNC / INHIBITOR / HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Betz, M. / Gomis-Rueth, F.X. / Bode, W. | ||||||
![]() | ![]() Title: 1.8-A crystal structure of the catalytic domain of human neutrophil collagenase (matrix metalloproteinase-8) complexed with a peptidomimetic hydroxamate primed-side inhibitor with a distinct selectivity profile. Authors: Betz, M. / Huxley, P. / Davies, S.J. / Mushtaq, Y. / Pieper, M. / Tschesche, H. / Bode, W. / Gomis-Ruth, F.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.7 KB | Display | ![]() |
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Full document | ![]() | 412.3 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18258.918 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: OBTAINED AS INCLUSION BODIES AND BY POSTERIOR REFOLDING Production host: ![]() ![]() |
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-Non-polymers , 5 types, 315 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HLE.gif)
![](data/chem/img/RIN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HLE.gif)
![](data/chem/img/RIN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | Resolution: 1.81→20 Å / Num. obs: 35353 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Num. measured all: 150360 |
Reflection shell | *PLUS Highest resolution: 1.81 Å / Lowest resolution: 1.87 Å / % possible obs: 96.7 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 25.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |