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- PDB-3e4e: Human cytochrome P450 2E1 in complex with the inhibitor 4-methylp... -

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Basic information

Entry
Database: PDB / ID: 3e4e
TitleHuman cytochrome P450 2E1 in complex with the inhibitor 4-methylpyrazole
ComponentsCytochrome P450 2E1
KeywordsOXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / acetaminophen / heme / Endoplasmic reticulum / Iron / Membrane / Metal-binding / Microsome
Function / homology
Function and homology information


: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonic acid epoxygenase activity ...: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / lipid hydroxylation / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / : / Xenobiotics / Paracetamol ADME / 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 / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / monooxygenase activity / xenobiotic metabolic process / response to bacterium / Hsp90 protein binding / oxygen binding / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2E-like / 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
4-methyl-1H-pyrazole / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMeneely, K.M. / Porubsky, P.R. / Scott, E.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of human cytochrome P450 2E1: insights into the binding of inhibitors and both small molecular weight and fatty acid substrates.
Authors: Porubsky, P.R. / Meneely, K.M. / Scott, E.E.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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 2E1
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5146
Polymers110,1172
Non-polymers1,3974
Water1,18966
1
A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7573
Polymers55,0581
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7573
Polymers55,0581
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.193, 71.193, 225.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cytochrome P450 2E1 / CYPIIE1 / P450-J


Mass: 55058.488 Da / Num. of mol.: 2 / Fragment: UNP residues 32 to 493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2E1, CYP2E / Plasmid: pKK2E1dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP-3 / References: UniProt: P05181, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-4PZ / 4-methyl-1H-pyrazole


Mass: 82.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 12% iso-propanol, 14% PEG 2000 MME, 0.1 M NaHEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2008 / Details: MIRRORS
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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→113.2 Å / Num. obs: 32629 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.3
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CYP2E1 IN COMPLEX WITH INDAZOLE (PDB ENTRY 3E6I)

3e6i


Resolution: 2.6→38.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / SU B: 12.893 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 1.077 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1767 5.1 %RANDOM
Rwork0.197 ---
obs0.201 32629 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7543 0 98 66 7707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0212.00810681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7195920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87823.12375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.916151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6961559
X-RAY DIFFRACTIONr_chiral_restr0.1280.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026051
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.23902
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.25317
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8431.54737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48527543
X-RAY DIFFRACTIONr_scbond_it2.39233485
X-RAY DIFFRACTIONr_scangle_it3.8224.53138
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% reflection
Rfree0.398 141 -
Rwork0.276 2396 -
obs--100 %

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