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- PDB-1z10: Crystal Structure of Human Microsomal P450 2A6 with Coumarin Bound -

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Basic information

Entry
Database: PDB / ID: 1z10
TitleCrystal Structure of Human Microsomal P450 2A6 with Coumarin Bound
Componentscytochrome P450, family 2, subfamily A, polypeptide 6
KeywordsOXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / monooxygenase / drug metabolizing enzyme / coumarin 7-hydroxylase / nicotine oxidase / heme
Function / homology
Function and homology information


coumarin catabolic process / coumarin 7-hydroxylase activity / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / 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 / cytoplasmic microtubule ...coumarin catabolic process / coumarin 7-hydroxylase activity / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / 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 / cytoplasmic microtubule / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / 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
COUMARIN / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYano, J.K. / Hsu, M.H. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen
Authors: Yano, J.K. / Hsu, M.H. / Griffin, K.J. / Stout, C.D. / Johnson, E.F.
History
DepositionMar 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Residues 1-28 were replaced with the sequence MAKKTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cytochrome P450, family 2, subfamily A, polypeptide 6
B: cytochrome P450, family 2, subfamily A, polypeptide 6
C: cytochrome P450, family 2, subfamily A, polypeptide 6
D: cytochrome P450, family 2, subfamily A, polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,82913
Polymers218,6874
Non-polymers3,1439
Water14,700816
1
A: cytochrome P450, family 2, subfamily A, polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4343
Polymers54,6721
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cytochrome P450, family 2, subfamily A, polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5264
Polymers54,6721
Non-polymers8553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cytochrome P450, family 2, subfamily A, polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4343
Polymers54,6721
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cytochrome P450, family 2, subfamily A, polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4343
Polymers54,6721
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.615, 157.591, 103.541
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly has not been determined but thought to be a monomer

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Components

#1: Protein
cytochrome P450, family 2, subfamily A, polypeptide 6


Mass: 54671.637 Da / Num. of mol.: 4 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A6 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5 alpha / References: UniProt: P11509, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-COU / COUMARIN / 2H-1-BENZOPYRAN-2-ONE


Mass: 146.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H6O2
#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.: 816 / 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: 2.6 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG3350, Tris, ammonium sulfate, Anapoe-X-405, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2004
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 177337 / Num. obs: 174569 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ2.pdb

1pq2


Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 8261 -RANDOM
Rwork0.194 ---
all0.196 177337 --
obs0.196 164494 92.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15029 0 222 816 16067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_dihedral_angle_d21.94
X-RAY DIFFRACTIONc_bond_d0.019

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