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- PDB-5om7: Crystal structure of Alpha1-antichymotrypsin variant DBS-II: a dr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5om7 | |||||||||
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Title | Crystal structure of Alpha1-antichymotrypsin variant DBS-II: a drug-binding serpin for doxorubicin | |||||||||
![]() | (Alpha-1-antichymotrypsin) x 2 | |||||||||
![]() | TRANSPORT PROTEIN / Serpin / Alpha1-antichymotrypsin / Doxorubicin-binding protein / protein design | |||||||||
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. / Kern, A. / 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 | ![]() | 98.3 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.6 KB | Display | ![]() |
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Full document | ![]() | 798.7 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5om2C ![]() 5om3C ![]() 5om5C ![]() 5om6C ![]() 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: 41900.398 Da / Num. of mol.: 1 Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N 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: 4720.580 Da / Num. of mol.: 1 Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N 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-DM2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20 % 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: Sep 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→42.231 Å / Num. obs: 42863 / % possible obs: 99.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6786 / CC1/2: 0.893 / Rrim(I) all: 0.936 / % possible all: 98.8 |
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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: 1.727→42.231 Å
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Refine LS restraints |
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LS refinement shell |
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