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- PDB-1t9s: Catalytic Domain Of Human Phosphodiesterase 5A in Complex with GMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 1t9s | ||||||
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Title | Catalytic Domain Of Human Phosphodiesterase 5A in Complex with GMP | ||||||
![]() | cGMP-specific 3',5'-cyclic phosphodiesterase | ||||||
![]() | HYDROLASE / PDE5A | ||||||
Function / homology | ![]() positive regulation of oocyte development / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / RHOBTB1 GTPase cycle / relaxation of cardiac muscle / cGMP catabolic process ...positive regulation of oocyte development / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / RHOBTB1 GTPase cycle / relaxation of cardiac muscle / cGMP catabolic process / positive regulation of cardiac muscle hypertrophy / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / Smooth Muscle Contraction / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / negative regulation of T cell proliferation / T cell proliferation / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, K.Y.J. / Card, G.L. / Suzuki, Y. / Artis, D.R. / Fong, D. / Gillette, S. / Hsieh, D. / Neiman, J. / West, B.L. / Zhang, C. ...Zhang, K.Y.J. / Card, G.L. / Suzuki, Y. / Artis, D.R. / Fong, D. / Gillette, S. / Hsieh, D. / Neiman, J. / West, B.L. / Zhang, C. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Bollag, G. | ||||||
![]() | ![]() Title: A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases Authors: Zhang, K.Y.J. / Card, G.L. / Suzuki, Y. / Artis, D.R. / Fong, D. / Gillette, S. / Hsieh, D. / Neiman, J. / West, B.L. / Zhang, C. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Bollag, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.5 KB | Display | ![]() |
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PDB format | ![]() | 122 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1t9rSC ![]() 1tazC ![]() 1tb5C ![]() 1tb7C ![]() 1tbbC ![]() 1tbfC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 535 - 857 / Label seq-ID: 23 - 346
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Details | The biological assembly is one monomer. |
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Components
#1: Protein | Mass: 39911.789 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O76074, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→69.01 Å / Num. all: 48496 / Num. obs: 48496 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.052 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3719 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1T9R Resolution: 2→69.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.116 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.151 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.597 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→69.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5055 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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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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