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- PDB-1pq2: Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8 -

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Basic information

Entry
Database: PDB / ID: 1pq2
TitleCrystal Structure of Human Drug Metabolizing Cytochrome P450 2C8
ComponentsCytochrome P450 2C8
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / CYP2C8 / MEMBRANE PROTEIN / TAXOL 6-HYDROXYLASE
Function / homology
Function and homology information


organic acid metabolic process / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / icosanoid biosynthetic process / 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 / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / icosanoid biosynthetic process / 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) / Xenobiotics / oxidative demethylation / 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 / retinoic acid metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PALMITIC ACID / PHOSPHATE ION / Cytochrome P450 2C8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchoch, G.A. / Yano, J.K. / Wester, M.R. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site
Authors: Schoch, G.A. / Yano, J.K. / Wester, M.R. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
History
DepositionJun 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 2C8
B: Cytochrome P450 2C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9497
Polymers108,1082
Non-polymers1,8415
Water66737
1
A: Cytochrome P450 2C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0224
Polymers54,0541
Non-polymers9683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9273
Polymers54,0541
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.988, 137.405, 97.322
Angle α, β, γ (deg.)90.00, 112.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytochrome P450 2C8 / CYPIIC8 / P450 form 1 / P450 MP- 12/MP-20 / P450 IIC2 / S-mephenytoin 4-hydroxylase


Mass: 54054.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2C8 / Production host: Escherichia coli (E. coli) / References: UniProt: P10632, unspecific monooxygenase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ETHANOL, PEG 4000, HEPES, SODIUM CHLORIDE, CYMAL-6 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.12 mMCYMAL-6 detergent1reservoir
240 mMpotassium phosphate1reservoirpH7.4
3400 mM1reservoirNaCl
40.8 mMEDTA1reservoir
50.16 mMdithiothreitol1reservoir
616 %glycerol1reservoir
7100 mMHEPES1reservoirpH7.5
815 %ethanol1reservoir
910 %PEG40001reservoir
10100 mMHEPES1droppH7.5
1115 %ethanol1drop
1210 %PEG40001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. all: 82164 / Num. obs: 38682 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 0.052 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.3 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Num. obs: 34573 / % possible obs: 97.5 % / Num. measured all: 79013 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.512

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N6B

1n6b


Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1751 5 %RANDOM
Rwork0.248 ---
all0.249 81039 --
obs0.248 34573 97.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.497 Å0.4226 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5489 Å0.4933 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 127 37 7550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010994
X-RAY DIFFRACTIONc_angle_deg1.65176
X-RAY DIFFRACTIONc_dihedral_angle_d23.03231
X-RAY DIFFRACTIONc_improper_angle_d1.56201
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.03231
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.56201

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