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- PDB-5uwl: Matrix metalloproteinase-13 complexed with selective inhibitor co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uwl | ||||||
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Title | Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a | ||||||
![]() | 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 | ![]() | 83.3 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 910.4 KB | Display | ![]() |
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Full document | ![]() | 913.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uwkC ![]() 5uwmC ![]() 5uwnC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19366.578 Da / Num. of mol.: 2 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 | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M sodium chloride, 0.1 M Tris pH 7, 1.0 M sodium citrate |
-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: 2.55→60.07 Å / Num. obs: 23277 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.1 Å2 / Rpim(I) all: 0.047 / Rsym value: 0.124 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3333 / Rpim(I) all: 0.369 / Rsym value: 0.967 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4L19 Resolution: 2.55→60.07 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→60.07 Å
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Refine LS restraints |
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LS refinement shell |
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