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- PDB-5uwn: Matrix metalloproteinase-13 complexed with selective inhibitor co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uwn | ||||||
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Title | Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d | ||||||
![]() | Collagenase 3 | ||||||
![]() | hydrolase/hydrolase inhibitor / Metalloproteinase / collagenase / MMP-13 / hydrolase / hydrolase-hydrolase inhibitor complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Taylor, A.B. / Cao, X. / Hart, P.J. | ||||||
![]() | ![]() Title: Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. Authors: Choi, J.Y. / Fuerst, R. / Knapinska, A.M. / Taylor, A.B. / Smith, L. / Cao, X. / Hart, P.J. / Fields, G.B. / Roush, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.4 KB | Display | ![]() |
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PDB format | ![]() | 145.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 43.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uwkC ![]() 5uwlC ![]() 5uwmC ![]() 4l19S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19366.578 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN (UNP RESIDUES 104-274) / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-8O7 / #5: Chemical | ChemComp-SO4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.88 Å3/Da / Density % sol: 74.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→125.66 Å / Num. obs: 30172 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 60.8 Å2 / Rpim(I) all: 0.12 / Rsym value: 0.244 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4397 / Rpim(I) all: 0.506 / Rsym value: 1.03 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4L19 Resolution: 3.2→95.8 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.05
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→95.8 Å
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Refine LS restraints |
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LS refinement shell |
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