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- PDB-1og2: Structure of human cytochrome P450 CYP2C9 -

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Basic information

Entry
Database: PDB / ID: 1og2
TitleStructure of human cytochrome P450 CYP2C9
ComponentsCYTOCHROME P450 2C9
KeywordsELECTRON TRANSPORT / DRUG METABOLISM / OXIDOREDUCTASE / HEME / MONOOXYGENASE
Function / homology
Function and homology information


arachidonate 14,15-epoxygenase activity / arachidonate 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 ...arachidonate 14,15-epoxygenase activity / arachidonate 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 / arachidonate epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / caffeine oxidase activity / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / oxidative demethylation / Xenobiotics / steroid hydroxylase activity / 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 / xenobiotic catabolic process / xenobiotic metabolic process / cholesterol metabolic process / monooxygenase activity / 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
HEME C / Cytochrome P450 2C9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWilliams, P.A. / Cosme, J. / Ward, A. / Angove, H.C. / Matak Vinkovic, D. / Jhoti, H.
CitationJournal: Nature / Year: 2003
Title: Crystal Structure of Human Cytochrome P450 2C9 with Bound Warfarin
Authors: Williams, P.A. / Cosme, J. / Ward, A. / Angove, H.C. / Matak Vinkovic, D. / Jhoti, H.
History
DepositionApr 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 2C9
B: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5744
Polymers108,3372
Non-polymers1,2372
Water2,648147
1
A: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7872
Polymers54,1691
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7872
Polymers54,1691
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.870, 164.870, 111.105
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8191, 0.5736, 0.0033), (-0.5736, -0.819, -0.0166), (-0.0068, -0.0155, 0.9999)
Vector: 27.584, 125.649, 10.794)

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Components

#1: Protein CYTOCHROME P450 2C9 / (R)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 7-MONOOXYGENASE / ...(R)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 6-MONOOXYGENASE / (S)-LIMONENE 7-MONOOXYGENASE / CYPIIC9 / CYTOCHROME P-450MP / CYTOCHROME P450 MP-4 / CYTOCHROME P450 MP-8 / CYTOCHROME P450 PB-1 / S-MEPHENYTOIN 4-HYDROXYLASE


Mass: 54168.590 Da / Num. of mol.: 2 / Fragment: SOLUBLE DOMAIN, RESIDUES 30-490 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE
References: UniProt: P11712, EC: 1.14.13.80, EC: 1.14.13.48, EC: 1.14.13.49
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYTOCHROMES P450 ARE HEME-THIOLATE MONOOXYGENASES THAT IN THE LIVER MICROSOMES FORM PART OF THE ...CYTOCHROMES P450 ARE HEME-THIOLATE MONOOXYGENASES THAT IN THE LIVER MICROSOMES FORM PART OF THE NADPH-DEPENDENT ELECTRON TRANSPORT PATHWAY. THE ENZYME OXIDIZES A VARIETY OF STRUCTURALLY UNRELATED COMPOUNDS, INCLUDING STEROIDS, FATTY ACIDS AND XENOBIOTICS. ENGINEERED RESIDUE IN CHAIN A, LYS 206 TO GLU ENGINEERED RESIDUE IN CHAIN A, ILE 215 TO VAL ENGINEERED RESIDUE IN CHAIN A, CYS 216 TO TYR ENGINEERED RESIDUE IN CHAIN A, SER 220 TO PRO ENGINEERED RESIDUE IN CHAIN A, PRO 221 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 222 TO LEU ENGINEERED RESIDUE IN CHAIN A, ILE 223 TO LEU ENGINEERED RESIDUE IN CHAIN B, LYS 206 TO GLU ENGINEERED RESIDUE IN CHAIN B, ILE 215 TO VAL ENGINEERED RESIDUE IN CHAIN B, CYS 216 TO TYR ENGINEERED RESIDUE IN CHAIN B, SER 220 TO PRO ENGINEERED RESIDUE IN CHAIN B, PRO 221 TO ALA ENGINEERED RESIDUE IN CHAIN B, ILE 222 TO LEU ENGINEERED RESIDUE IN CHAIN B, ILE 223 TO LEU
Sequence detailsRESIDUES 1-29 OF THE FULL LENGTH PROTEIN WERE DELETED (THE PROPOSED TRANSMEMBRANE DOMAIN) AND A ...RESIDUES 1-29 OF THE FULL LENGTH PROTEIN WERE DELETED (THE PROPOSED TRANSMEMBRANE DOMAIN) AND A SHORT REGION OF SEQUENCE INTRODUCED TO ASSIST WITH EXPRESSION. A FOUR-HISTIDINE TAG WAS INTRODUCED AT THE C-TERMINUS FOR PURIFICATION PURPOSES

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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: 4.02 Å3/Da / Density % sol: 70 %
Crystal growpH: 8.4 / Details: pH 8.40
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
210 mMpotassium phosphate1droppH7.4
30.5 M1dropKCl
420 %(v/v)glycerol1drop
51 mMEDTA1drop
62 mMdithiothreitol1drop
70.1 MTris1reservoirpH8.4
815-25 %(v/v)PEG4001reservoir
95-12.5 %(w/v)PEG80001reservoir
1010 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 51912 / % possible obs: 96.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.21 / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / Redundancy: 2.6 % / Num. measured all: 340743 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 96.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.21

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT6

1dt6


Resolution: 2.6→55.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.96 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2628 5.1 %RANDOM
Rwork0.208 ---
obs0.21 49246 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 86 147 7619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227662
X-RAY DIFFRACTIONr_bond_other_d0.0040.026948
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.98110380
X-RAY DIFFRACTIONr_angle_other_deg0.891316256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028356
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021526
X-RAY DIFFRACTIONr_nbd_refined0.2150.21939
X-RAY DIFFRACTIONr_nbd_other0.2280.28055
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.24574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.64154620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.23667528
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.37763042
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3487.52852
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.407 186
Rwork0.364 2950
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.76

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