+Open data
-Basic information
Entry | Database: PDB / ID: 1nr6 | ||||||
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Title | MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH DICLOFENAC | ||||||
Components | CYTOCHROME P450 2C5 | ||||||
Keywords | OXIDOREDUCTASE / MEMBRANE PROTEIN / PROGESTERONE 21-HYDROXYLASE / BENZO(A) / PYRENE HYDROXYLASE / ESTRADIOL 2-HYDROXYLASE / P450 / CYP2C5 / DICLOFENAC COMPLEX | ||||||
Function / homology | Function and homology information organic acid metabolic process / unspecific monooxygenase / aromatase activity / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wester, M.R. / Johnson, E.F. / Stout, C.D. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structure of Mammalian Cytochrome P450 2C5 Complexed with Diclofenac at 2.1 A Resolution: Evidence for an Induced Fit Model of Substrate Binding Authors: WESTER, M.R. / JOHNSON, E.F. / Marques-Soares, C. / Dijols, S. / Dansette, P.M. / Mansuy, D. / STOUT, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nr6.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nr6.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 1nr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nr6_validation.pdf.gz | 545.4 KB | Display | wwPDB validaton report |
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Full document | 1nr6_full_validation.pdf.gz | 555.2 KB | Display | |
Data in XML | 1nr6_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1nr6_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/1nr6 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/1nr6 | HTTPS FTP |
-Related structure data
Related structure data | 1n6bS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 53884.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2C5 / Plasmid: PCW / Production host: Escherichia coli (E. coli) / References: UniProt: P00179, unspecific monooxygenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-DIF / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: AMMONIUM SULFATE, CYMAL5, pH 7.0, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2001 |
Radiation | Monochromator: FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 48402 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.565 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 185186 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N6B Resolution: 2.1→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.2 Å2 | ||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |