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- PDB-6kd5: Crystal structure of the extracellular domain of MSPL/TMPRSS13 in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kd5 | |||||||||||||||||||||||||||
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Title | Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor | |||||||||||||||||||||||||||
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![]() | STRUCTURAL PROTEIN/INHIBITOR / HYDROLASE / STRUCTURAL PROTEIN-INHIBITOR complex | |||||||||||||||||||||||||||
Function / homology | ![]() scavenger receptor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / membrane => GO:0016020 / blood microparticle / serine-type endopeptidase activity Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() synthetic construct (others) | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Ohno, A. / Maita, N. / Okumura, Y. / Nikawa, T. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza. Authors: Ohno, A. / Maita, N. / Tabata, T. / Nagano, H. / Arita, K. / Ariyoshi, M. / Uchida, T. / Nakao, R. / Ulla, A. / Sugiura, K. / Kishimoto, K. / Teshima-Kondo, S. / Okumura, Y. / Nikawa, T. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1010.5 KB | Display | ![]() |
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Full document | ![]() | 1016.3 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2anyS 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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Unit cell |
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Components
-Transmembrane protease serine ... , 2 types, 2 molecules AB
#1: Protein | Mass: 18165.039 Da / Num. of mol.: 1 / Fragment: UNP residues 192-325 Source method: isolated from a genetically manipulated source Details: Non-catalytic chain / Source: (gene. exp.) ![]() ![]() References: UniProt: Q9BYE2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 28771.436 Da / Num. of mol.: 1 / Fragment: UNP residues 326-586 Source method: isolated from a genetically manipulated source Details: Catalytic chain / Source: (gene. exp.) ![]() ![]() References: UniProt: Q9BYE2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 749.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 89 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CA / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | This protein is cleaved at between Arg320-Ile321, then turns into a mature form. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 64.9 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES(pH7.5), 2.4M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 19249 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.088 / Rrim(I) all: 0.175 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2303 / CC1/2: 0.729 / Rpim(I) all: 0.593 / Rrim(I) all: 1.174 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ANY Resolution: 2.6→39.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.564 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.266 / 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: 33.142 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→39.99 Å
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Refine LS restraints |
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