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- PDB-1og5: Structure of human cytochrome P450 CYP2C9 -

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Basic information

Entry
Database: PDB / ID: 1og5
TitleStructure of human cytochrome P450 CYP2C9
ComponentsCYTOCHROME P450 2C9
KeywordsELECTRON TRANSPORT / DRUG METABOLISM / OXIDOREDUCTASE / HEME / MONOOXYGENASE
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 / xenobiotic metabolic process / cholesterol 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
HEME C / S-WARFARIN / Cytochrome P450 2C9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 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 24, 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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)110,1916
Polymers108,3372
Non-polymers1,8544
Water7,620423
1
A: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0953
Polymers54,1691
Non-polymers9272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450 2C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0953
Polymers54,1691
Non-polymers9272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.757, 164.757, 110.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8214, -0.5704, 0.0004), (0.5704, -0.8214, -0.0033), (0.0022, -0.0025, 1)
Vector: -28.186, 125.507, -9.333)

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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: Chemical ChemComp-SWF / S-WARFARIN


Mass: 308.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16O4 / Comment: medication, anticoagulant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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 1-30 OF THE FULL LENGTH PROTEIN WERE DELETED (THE PROPOSED TRANSMEMBRANE DOMAIN) AND A ...RESIDUES 1-30 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: 4.01 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: 2.55→50 Å / Num. obs: 56722 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.55 Å / Lowest resolution: 50 Å / % possible obs: 100 % / Redundancy: 5.6 % / Num. measured all: 1507766 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNX2002refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.55→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2874 5.1 %RANDOM
Rwork0.2247 ---
obs-56722 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 132 423 7939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014114
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_deg1.76244
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.76

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