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- PDB-2vn0: CYP2C8DH COMPLEXED WITH TROGLITAZONE -

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Basic information

Entry
Database: PDB / ID: 2vn0
TitleCYP2C8DH COMPLEXED WITH TROGLITAZONE
ComponentsCYTOCHROME P450 2C8
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / ENDOPLASMIC RETICULUM / METAL-BINDING / PALMITIC ACID / HUMAN P450 2C8 / TROGLITAZONE / POLYMORPHISM / MONOOXYGENASE / IRON / HEME / CYP2C8 / MEMBRANE / MICROSOME / MONOOXYGENASES / INHIBITOR COMPLEX
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
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 / Chem-TDZ / 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. / Sansen, S. / Stout, C.D. / Johnson, E.F.
CitationJournal: 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
DepositionJan 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 2C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3694
Polymers54,0541
Non-polymers1,3143
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.200, 136.090, 163.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 28-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P10632, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TDZ / (5R)-5-(4-{[(2R)-6-HYDROXY-2,5,7,8-TETRAMETHYL-3,4-DIHYDRO-2H-CHROMEN-2-YL]METHOXY}BENZYL)-1,3-THIAZOLIDINE-2,4-DIONE / TROGLITAZONE


Mass: 441.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27NO5S / Comment: antiinflammatory*YM
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREPLACEMENT OF RESIDUES 1-27 WITH THE SEQUENCE MAKKTSSKG, ADDITION OF A C-TERMINAL 4 RESIDUE ...REPLACEMENT OF RESIDUES 1-27 WITH THE SEQUENCE MAKKTSSKG, ADDITION OF A C-TERMINAL 4 RESIDUE HISTIDINE TAG (RESIDUES 491-494)

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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: 3.82 Å3/Da / Density % sol: 67.8 % / Description: NONE
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC CCD / Detector: CCD / Date: May 12, 2006
Details: VERTICAL FOCUSING MIRROR SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
RadiationMonochromator: SIDE-SCATTERING CUBEROOT I- BEAM BENT SINGLE CRYSTAL ASYMETRIC CUT 12.2 DEGS.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→47.9 Å / Num. obs: 23135 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PQ2

1pq2


Resolution: 2.7→43.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1634289.67 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1167 5 %RANDOM
Rwork0.218 ---
obs0.218 23134 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8352 Å2 / ksol: 0.340176 e/Å3
Displacement parametersBiso mean: 56.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.88 Å20 Å20 Å2
2--12.9 Å20 Å2
3----7.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 92 30 3825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 193 5.1 %
Rwork0.316 3609 -
obs--100 %

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