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- PDB-3t3s: Human Cytochrome P450 2A13 in complex with Pilocarpine -

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Basic information

Entry
Database: PDB / ID: 3t3s
TitleHuman Cytochrome P450 2A13 in complex with Pilocarpine
ComponentsCytochrome P450 2A13
KeywordsOXIDOREDUCTASE / CYP2A13 / cytochrome P450 2A13 / P450 2A13 / heme protein / monooxygenase / drug metabolism / xenobiotic metabolism / endoplasmic reticulum / membrane
Function / homology
Function and homology information


coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / 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 ...coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / 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 / unspecific monooxygenase / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2A-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 ...Cytochrome P450, E-class, group I, CYP2A-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
Chem-9PL / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDeVore, N.M. / Scott, E.E.
CitationJournal: Febs J. / Year: 2012
Title: Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine.
Authors: DeVore, N.M. / Meneely, K.M. / Bart, A.G. / Stephens, E.S. / Battaile, K.P. / Scott, E.E.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_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_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_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 2A13
B: Cytochrome P450 2A13
C: Cytochrome P450 2A13
D: Cytochrome P450 2A13
E: Cytochrome P450 2A13
F: Cytochrome P450 2A13
G: Cytochrome P450 2A13
H: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,62022
Polymers438,4388
Non-polymers6,18114
Water57632
1
A: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6303
Polymers54,8051
Non-polymers8252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6303
Polymers54,8051
Non-polymers8252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6303
Polymers54,8051
Non-polymers8252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6303
Polymers54,8051
Non-polymers8252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6303
Polymers54,8051
Non-polymers8252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6303
Polymers54,8051
Non-polymers8252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4212
Polymers54,8051
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cytochrome P450 2A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4212
Polymers54,8051
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.501, 119.862, 154.871
Angle α, β, γ (deg.)101.01, 101.72, 93.59
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome P450 2A13 / CYPIIA13


Mass: 54804.758 Da / Num. of mol.: 8 / Fragment: unp residues 31-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A13 / Plasmid: pKK2A13dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: Q16696, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-9PL / (3S,4R)-3-ethyl-4-[(1-methyl-1H-imidazol-5-yl)methyl]dihydrofuran-2(3H)-one / PILOCARPINE


Mass: 208.257 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H16N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 30% PEG 3350, 0.175 M Tris, pH 8.5, and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 28, 2010 / Details: RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→117 Å / Num. obs: 96716 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.117 / Rsym value: 0.135 / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERMRphasing
REFMAC6.1.13refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FDV

2fdv


Resolution: 3→102.88 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.835 / SU B: 22.607 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.536
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.303 4826 5 %RANDOM
Rwork0.213 ---
obs0.218 91882 98.3 %-
all-91882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2--0.02 Å2-0.02 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 3→102.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30017 0 434 32 30483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02231287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.99842264
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97553704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94723.1261542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.501155371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.38715255
X-RAY DIFFRACTIONr_chiral_restr0.1110.24343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02124227
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5511.518496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.029229889
X-RAY DIFFRACTIONr_scbond_it1.408312791
X-RAY DIFFRACTIONr_scangle_it2.2894.512375
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 344 -
Rwork0.29 6761 -
obs--97.87 %

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