+Open data
-Basic information
Entry | Database: PDB / ID: 7lad | ||||||
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Title | Clobetasol propionate bound to CYP3A5 | ||||||
Components | Cytochrome P450 3A5 | ||||||
Keywords | MEMBRANE PROTEIN / Cytochrome P450 / CYP3A5 | ||||||
Function / homology | Function and homology information testosterone 6-beta-hydroxylase activity / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / Aflatoxin activation and detoxification / Xenobiotics / oxidative demethylation / estrogen metabolic process ...testosterone 6-beta-hydroxylase activity / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / Aflatoxin activation and detoxification / Xenobiotics / oxidative demethylation / estrogen metabolic process / retinoic acid metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / oxygen binding / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Buchman, C.D. / Miller, D. / Wang, J. / Jayaraman, S. / Chen, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Unraveling the Structural Basis of Selective Inhibition of Human Cytochrome P450 3A5. Authors: Wang, J. / Buchman, C.D. / Seetharaman, J. / Miller, D.J. / Huber, A.D. / Wu, J. / Chai, S.C. / Garcia-Maldonado, E. / Wright, W.C. / Chenge, J. / Chen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lad.cif.gz | 226.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lad.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/7lad ftp://data.pdbj.org/pub/pdb/validation_reports/la/7lad | HTTPS FTP |
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-Related structure data
Related structure data | 6mjmS 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: 55069.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A5 / Production host: Escherichia coli (E. coli) / References: UniProt: P20815, unspecific monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-XRD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M ADA, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.646→29.4 Å / Num. obs: 14710 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.65→2.71 Å / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1043 / CC1/2: 0.827 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MJM Resolution: 2.65→29.4 Å / SU ML: 0.4016 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.3288 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: 65.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→29.4 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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