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Yorodumi- PDB-4ajd: Identification and structural characterization of PDE10 fragment ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ajd | ||||||
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Title | Identification and structural characterization of PDE10 fragment inhibitors | ||||||
Components | CAMP AND CAMP-INHIBITED CGMP 3', 5'-CYCLIC PHOSPHODIESTERASE 10A, PDE10 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity ...cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cAMP-mediated signaling / G alpha (s) signalling events / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Johansson, P. / Albert, J.S. / Spadola, L. / Akerud, T. / Back, E. / Hillertz, P. / Horsefeld, R. / Scott, C. / Spear, N. / Tian, G. ...Johansson, P. / Albert, J.S. / Spadola, L. / Akerud, T. / Back, E. / Hillertz, P. / Horsefeld, R. / Scott, C. / Spear, N. / Tian, G. / Tigerstrom, A. / Aharony, D. / Geschwindner, S. | ||||||
Citation | Journal: To be Published Title: Identification and Structural Characterization of Pde10 Fragment Inhibitors Authors: Johansson, P. / Albert, J.S. / Spadola, L. / Akerud, T. / Back, E. / Hillertz, P. / Horsefeld, R. / Scott, C. / Spear, N. / Tian, G. / Tigerstrom, A. / Aharony, D. / Geschwindner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ajd.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ajd.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ajd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ajd_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 4ajd_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 4ajd_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 4ajd_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/4ajd ftp://data.pdbj.org/pub/pdb/validation_reports/aj/4ajd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.174, -0.943, -0.284), Vector: |
-Components
#1: Protein | Mass: 37934.602 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 439-764 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.15 % / Description: NONE |
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Crystal grow | pH: 7 Details: 13-18% PEG3350, 4-10 MM TCEP, 100 MM HEPES PH 7.5 AND 200MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.32 Å / Num. obs: 38555 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 36.62 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.4 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.9156 / Cor.coef. Fo:Fc free: 0.8709 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG F04. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5587. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG F04. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5587. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=28. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
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Displacement parameters | Biso mean: 35.96 Å2
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Refine analyze | Luzzati coordinate error obs: 0.271 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 15
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