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- PDB-5d63: MOA-Z-VAD-fmk inhibitor complex, direct/inverted dual orientation -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d63 | |||||||||
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Title | MOA-Z-VAD-fmk inhibitor complex, direct/inverted dual orientation | |||||||||
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![]() | HYDROLASE / papain-like / inhibitor / protease / fungal | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cordara, G. / Krengel, U. | |||||||||
![]() | ![]() Title: An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor. Authors: Cordara, G. / van Eerde, A. / Grahn, E.M. / Winter, H.C. / Goldstein, I.J. / Krengel, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 63.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d61C ![]() 5d62C ![]() 3ef2S S: Starting model for refinement 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AL
#1: Protein | Mass: 32328.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: fairy rings mushroom Source: (gene. exp.) ![]() Plasmid: pT7-LO / Details (production host): IPTG-inducible / Production host: ![]() ![]() |
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#2: Protein/peptide | |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 288 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.84 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M imidazole pH 8.0, 16% PEG 8000, 5% DMSO, 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.42 Å / Num. all: 48993 / Num. obs: 48993 / % possible obs: 93.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 70.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EF2 Resolution: 1.65→46.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.429 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / 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: 14.127 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→46.42 Å
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Refine LS restraints |
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