+Open data
-Basic information
Entry | Database: PDB / ID: 2nnj | ||||||
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Title | CYP2C8dH complexed with felodipine | ||||||
Components | Cytochrome P450 2C8 | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / CYP2C8 / Human P450 2C8 / monooxygenases / Felodipine / Plendil / inhibitor complex / palmitic acid | ||||||
Function / homology | Function and homology information organic acid metabolic process / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / CYP2E1 reactions / arachidonic acid epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity ...organic acid metabolic process / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / CYP2E1 reactions / arachidonic acid epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / Biosynthesis of maresin-like SPMs / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / oxidative demethylation / Xenobiotics / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / long-chain fatty acid biosynthetic process / estrogen metabolic process / retinol metabolic process / retinoic acid metabolic process / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / xenobiotic catabolic process / monooxygenase activity / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Schoch, G.A. / Yano, J.K. / Stout, C.D. / Johnson, E.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid. Authors: Schoch, G.A. / Yano, J.K. / Sansen, S. / Dansette, P.M. / Stout, C.D. / Johnson, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nnj.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nnj.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 2nnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nnj_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2nnj_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2nnj_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 2nnj_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/2nnj ftp://data.pdbj.org/pub/pdb/validation_reports/nn/2nnj | HTTPS FTP |
-Related structure data
Related structure data | 2nnhC 2nniC 2vn0C 1pq2S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54054.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2C8 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / References: UniProt: P10632, unspecific monooxygenase |
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-Non-polymers , 5 types, 185 molecules
#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-225 / | #5: Chemical | ChemComp-PLM / | #6: 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: 3.91 Å3/Da / Density % sol: 68.53 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, HEPES, LiSO4, MeOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD Details: Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. all: 38962 / Num. obs: 38962 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.063 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.28→2.35 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.381 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PQ2 Resolution: 2.28→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.28→50 Å
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Refine LS restraints |
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