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- PDB-5om3: Crystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5om3 | ||||||
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Title | Crystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MMP14-cleavable drug-binding serpin for doxycycline | ||||||
![]() | (Alpha-1-antichymotrypsin) x 2 | ||||||
![]() | TRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / Doxycycline-binding protein / MMP14-cleavable RCL | ||||||
Function / homology | ![]() maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmidt, K. / Muller, Y.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein. Authors: Schmidt, K. / Gardill, B.R. / Kern, A. / Kirchweger, P. / Borsch, M. / Muller, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 809.3 KB | Display | ![]() |
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Full document | ![]() | 811.8 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5om2C ![]() 5om5C ![]() 5om6C ![]() 5om7C ![]() 5om8C ![]() 6ftpC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 41827.348 Da / Num. of mol.: 1 Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F V355L K356F T358P L360S S361L A362R L363M P382D T383H D384F Q386W N387S Source method: isolated from a genetically manipulated source Details: all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4878.847 Da / Num. of mol.: 1 Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F V355L K356F T358P L360S S361L A362R L363M P382D T383H D384F Q386W N387S Source method: isolated from a genetically manipulated source Details: all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-DXT / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.2 Å / Num. obs: 27859 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0109 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4407 / CC1/2: 0.856 / Rrim(I) all: 0.908 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.16 Å
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Refine LS restraints |
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LS refinement shell |
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