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- PDB-830c: COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID -
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Open data
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Basic information
Entry | Database: PDB / ID: 830c | ||||||
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Title | COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID | ||||||
![]() | MMP-13 | ||||||
![]() | MATRIX METALLOPROTEASE | ||||||
Function / homology | ![]() growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lovejoy, B. / Welch, A. / Carr, S. / Luong, C. / Broka, C. / Hendricks, R.T. / Campbell, J. / Walker, K. / Martin, R. / Van Wart, H. / Browner, M.F. | ||||||
![]() | ![]() Title: Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors. Authors: Lovejoy, B. / Welch, A.R. / Carr, S. / Luong, C. / Broka, C. / Hendricks, R.T. / Campbell, J.A. / Walker, K.A. / Martin, R. / Van Wart, H. / Browner, M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502 KB | Display | ![]() |
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Full document | ![]() | 506.8 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 456cC ![]() 966cC ![]() 1cgfS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 18909.076 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN IS COMPLEXED WITH A DIPHENYL-ETHER, SULPHONE INHIBITOR Source: (gene. exp.) ![]() Description: HUMAN CDNA CONSTRUCT. CDNA CONSTRUCT OF PROCOLLAGENASE-3 Production host: ![]() ![]() References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Dec 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 43128 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CGF Resolution: 1.6→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: INHIBITOR REFINED USING PARAMETERS DERIVED FROM QUANTA
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Displacement parameters | Biso mean: 14.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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