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- PDB-8h78: Crystal structure of human MMP-2 catalytic domain in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h78 | ||||||
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Title | Crystal structure of human MMP-2 catalytic domain in complex with inhibitor | ||||||
![]() | Matrix metalloproteinase-2 | ||||||
![]() | HYDROLASE / Gelatinase A / Matrix metalloproteinase-2 / 72 kDa type IV collagenase | ||||||
Function / homology | DIHYDROGENPHOSPHATE ION / Chem-L2U![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kamitani, M. / Takeuchi, T. / Mima, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold. Authors: Takeuchi, T. / Nomura, Y. / Tamita, T. / Nishikawa, R. / Kakinuma, H. / Kojima, N. / Hitaka, K. / Tamura, Y. / Kamitani, M. / Mima, M. / Nozoe, A. / Hayashi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 876 KB | Display | ![]() |
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Full document | ![]() | 887 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ayuS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 18809.893 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 44 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2HP.gif)
![](data/chem/img/L2U.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2HP.gif)
![](data/chem/img/L2U.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-2HP / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 16 % w/v Polyethylene glycol 8,000, 20 % v/v Glycerol, 40 mM Potassium di-hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→21.78 Å / Num. obs: 15535 / % possible obs: 99.8 % / Redundancy: 11.5 % / CC1/2: 0.976 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2252 / CC1/2: 0.567 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AYU Resolution: 2.4→21.78 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.844 / SU B: 17.224 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R: 0.58 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.291 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→21.78 Å
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Refine LS restraints |
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