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- PDB-1r9o: Crystal Structure of P4502C9 with Flurbiprofen bound -

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Basic information

Entry
Database: PDB / ID: 1r9o
TitleCrystal Structure of P4502C9 with Flurbiprofen bound
ComponentsCytochrome P450 2C9
KeywordsOXIDOREDUCTASE / P450 / monooxygenase / drug metabolizing enzyme / heme
Function / homology
Function and homology information


arachidonic acid 14,15-epoxygenase activity / arachidonic acid 11,12-epoxygenase activity / amide metabolic process / (S)-limonene 6-monooxygenase / (S)-limonene 7-monooxygenase / (R)-limonene 6-monooxygenase / (S)-limonene 6-monooxygenase activity / (S)-limonene 7-monooxygenase activity / (R)-limonene 6-monooxygenase activity / monocarboxylic acid metabolic process ...arachidonic acid 14,15-epoxygenase activity / arachidonic acid 11,12-epoxygenase activity / amide metabolic process / (S)-limonene 6-monooxygenase / (S)-limonene 7-monooxygenase / (R)-limonene 6-monooxygenase / (S)-limonene 6-monooxygenase activity / (S)-limonene 7-monooxygenase activity / (R)-limonene 6-monooxygenase activity / monocarboxylic acid metabolic process / urea 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 / caffeine oxidase activity / Biosynthesis of maresin-like SPMs / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / monoterpenoid metabolic process / 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 / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / steroid hydroxylase activity / xenobiotic catabolic process / monooxygenase activity / cholesterol metabolic process / xenobiotic metabolic process / oxidoreductase 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
FLURBIPROFEN / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2C9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWester, M.R. / Yano, J.K. / Schoch, G.A. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structure of Human Cytochrome P450 2C9 Complexed with Flurbiprofen at 2.0 A Resolution
Authors: Wester, M.R. / Yano, J.K. / Schoch, G.A. / Yang, C. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE FIRST 22 RESIDUES OF THE SWISS PROT REFERENCE SEQUENCE (ACCESSION CODE P11712) WERE ...SEQUENCE THE FIRST 22 RESIDUES OF THE SWISS PROT REFERENCE SEQUENCE (ACCESSION CODE P11712) WERE REPLACED BY RESIDUES MAKKT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2764
Polymers54,3231
Non-polymers9533
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.047, 91.047, 169.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cytochrome P450 2C9 / CYPIIC9 / P450 PB-1 / P450 MP-4 / S-mephenytoin 4-hydroxylase / P-450MP


Mass: 54322.887 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: I490V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2C9 / Plasmid: PCWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P11712, 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-FLP / FLURBIPROFEN


Mass: 244.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13FO2 / Comment: antiinflammatory*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Hepes, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2002
Details: Flat mirror (verticle focusing), single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 35440 / Num. obs: 35418 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.082 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2614 / Rsym value: 0.406 / % possible all: 99.9

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Processing

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

1n6b


Resolution: 2→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1772 -RANDOM
Rwork0.191 ---
all0.194 35396 --
obs0.194 35396 99.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 67 255 3972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.052
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d1.91
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.291 296 -
Rwork0.253 --
obs-5597 100 %

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