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Open data
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Basic information
Entry | Database: PDB / ID: 2h42 | ||||||
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Title | Crystal structure of PDE5 in complex with sildenafil | ||||||
![]() | cGMP-specific 3',5'-cyclic phosphodiesterase | ||||||
![]() | HYDROLASE / viagra / PDE5 | ||||||
Function / homology | ![]() positive regulation of oocyte development / 3',5'-cyclic-GMP phosphodiesterase / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / relaxation of cardiac muscle / RHOBTB1 GTPase cycle / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects ...positive regulation of oocyte development / 3',5'-cyclic-GMP phosphodiesterase / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / relaxation of cardiac muscle / RHOBTB1 GTPase cycle / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / Smooth Muscle Contraction / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / negative regulation of T cell proliferation / T cell proliferation / cAMP-mediated signaling / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Ke, H. | ||||||
![]() | ![]() Title: Multiple Conformations of Phosphodiesterase-5: Implications for enzyme function and drug development Authors: Wang, H. / Liu, Y. / Huai, Q. / Cai, J. / Zoraghi, R. / Francis, S.H. / Corbin, J.D. / Robinson, H. / Xin, Z. / Lin, G. / Ke, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.4 KB | Display | ![]() |
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PDB format | ![]() | 168.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2h40C ![]() 2h44C ![]() 1rkpS C: citing same article ( 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | Biological unit may be a monomer. However, the crystallographic asymmetric unit contains 3 molecules. |
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Components
#1: Protein | Mass: 37788.531 Da / Num. of mol.: 3 / Fragment: catalytic domain, residues 535-860 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O76074, 3',5'-cyclic-GMP 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: 3.33 Å3/Da / Density % sol: 63.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 mM sildenafil mixed with 15 mg/mL PDE5A1 overnight, crystallized against a well buffer of 1.0 M sodium citrate, 2.5% ethanol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 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: 2.3→30 Å / Num. obs: 68786 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RKP Resolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Xplor file |
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