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Yorodumi- PDB-5up0: Crystal structure of human PDE1B catalytic domain in complex with... -
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-Basic information
Entry | Database: PDB / ID: 5up0 | ||||||
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Title | Crystal structure of human PDE1B catalytic domain in complex with inhibitor 3 (6-(4-chlorobenzyl)-8,9,10,11-tetrahydrobenzo[4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one) | ||||||
Components | Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / hydrolase / hydrolase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cellular response to macrophage colony-stimulating factor stimulus / serotonin metabolic process / dopamine catabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / monocyte differentiation / Cam-PDE 1 activation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP effects ...calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cellular response to macrophage colony-stimulating factor stimulus / serotonin metabolic process / dopamine catabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / monocyte differentiation / Cam-PDE 1 activation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP effects / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / response to amphetamine / cAMP-mediated signaling / locomotory behavior / visual learning / G alpha (s) signalling events / calmodulin binding / neuronal cell body / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Cedervall, E.P. / Allerston, C.K. / Xu, R. / Sridhar, V. / Barker, R. / Aertgeerts, K. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties. Authors: Dyck, B. / Branstetter, B. / Gharbaoui, T. / Hudson, A.R. / Breitenbucher, J.G. / Gomez, L. / Botrous, I. / Marrone, T. / Barido, R. / Allerston, C.K. / Cedervall, E.P. / Xu, R. / Sridhar, V. ...Authors: Dyck, B. / Branstetter, B. / Gharbaoui, T. / Hudson, A.R. / Breitenbucher, J.G. / Gomez, L. / Botrous, I. / Marrone, T. / Barido, R. / Allerston, C.K. / Cedervall, E.P. / Xu, R. / Sridhar, V. / Barker, R. / Aertgeerts, K. / Schmelzer, K. / Neul, D. / Lee, D. / Massari, M.E. / Andersen, C.B. / Sebring, K. / Zhou, X. / Petroski, R. / Limberis, J. / Augustin, M. / Chun, L.E. / Edwards, T.E. / Peters, M. / Tabatabaei, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5up0.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5up0.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 5up0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5up0_validation.pdf.gz | 801.4 KB | Display | wwPDB validaton report |
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Full document | 5up0_full_validation.pdf.gz | 803.7 KB | Display | |
Data in XML | 5up0_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 5up0_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5up0 ftp://data.pdbj.org/pub/pdb/validation_reports/up/5up0 | HTTPS FTP |
-Related structure data
Related structure data | 5uoyC 5uwfC 1tazS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41279.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE1B, PDE1B1, PDES1B / Production host: Escherichia coli (E. coli) References: UniProt: Q01064, 3',5'-cyclic-nucleotide phosphodiesterase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-8HP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 3.1 M NaCl, 0.1 M HEPES pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→61.79 Å / Num. obs: 34119 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.024 / Rrim(I) all: 0.077 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.626 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2482 / CC1/2: 0.653 / Rpim(I) all: 0.525 / Rrim(I) all: 1.71 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TAZ Resolution: 2.04→61.788 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→61.788 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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