+Open data
-Basic information
Entry | Database: PDB / ID: 7faq | ||||||||||||
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Title | Crystal structure of PDE5A in complex with inhibitor L1 | ||||||||||||
Components | cGMP-specific 3',5'-cyclic phosphodiesterase | ||||||||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.20013606546 Å | ||||||||||||
Authors | Wu, D. / Huang, Y.Y. / Luo, H.B. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Acta Pharm Sin B / Year: 2022 Title: Free energy perturbation (FEP)-guided scaffold hopping. Authors: Wu, D. / Zheng, X. / Liu, R. / Li, Z. / Jiang, Z. / Zhou, Q. / Huang, Y. / Wu, X.N. / Zhang, C. / Huang, Y.Y. / Luo, H.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7faq.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7faq.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 7faq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/7faq ftp://data.pdbj.org/pub/pdb/validation_reports/fa/7faq | HTTPS FTP |
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-Related structure data
Related structure data | 7farC 4md6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40266.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE5A, PDE5 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: O76074, 3',5'-cyclic-GMP phosphodiesterase |
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-Non-polymers , 5 types, 76 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-2OI / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium sulfate, 0.1 M sodium cacodylate, pH 6.5, 17% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54056 Å |
Detector | Type: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Aug 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22.71 Å / Num. obs: 21798 / % possible obs: 99.81 % / Redundancy: 8.1 % / Biso Wilson estimate: 42.9547344485 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2186 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4md6 Resolution: 2.20013606546→22.7022391169 Å / SU ML: 0.304886308095 / Cross valid method: NONE / σ(F): 1.36058762158 / Phase error: 29.6972174003 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.9247361213 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20013606546→22.7022391169 Å
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Refine LS restraints |
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LS refinement shell |
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