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- PDB-1z11: Crystal Structure of Human Microsomal P450 2A6 with Methoxsalen Bound -

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Basic information

Entry
Database: PDB / ID: 1z11
TitleCrystal Structure of Human Microsomal P450 2A6 with Methoxsalen Bound
Componentscytochrome P450, family 2, subfamily A, polypeptide 6
KeywordsOXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / monooxygenase / drug metabolizing enzyme / coumarin 7-hydroxylase / nicotine oxidase / heme / methoxsalen
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 / arachidonic acid 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 / steroid metabolic process ...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 / arachidonic acid 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 / steroid metabolic process / cytoplasmic microtubule / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
METHOXSALEN / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: 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)222,01712
Polymers218,6874
Non-polymers3,3318
Water9,080504
1
A: cytochrome P450, family 2, subfamily A, polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5043
Polymers54,6721
Non-polymers8332
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)55,5043
Polymers54,6721
Non-polymers8332
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)55,5043
Polymers54,6721
Non-polymers8332
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)55,5043
Polymers54,6721
Non-polymers8332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.66, 159.03, 103.88
Angle α, β, γ (deg.)90.00, 92.00, 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-8MO / METHOXSALEN / 9-METHOXY-7H-FURO[3,2-G][1]BENZOPYRAN-7-ONE


Mass: 216.190 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8O4 / Comment: medication, toxin*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.7 Å3/Da / Density % sol: 51.8 %
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: BL9-2 / Wavelength: 1.03, 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2004 / Details: double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.031
20.981
ReflectionResolution: 2.05→50 Å / Num. all: 143181 / Num. obs: 140326 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.6 / Num. unique all: 12584 / % possible all: 88.9

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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: Coumarin complex of CYP2A6, pdb entry 1Z10

1z10


Resolution: 2.05→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 5445 -RANDOM
Rwork0.2194 ---
all0.2211 143181 --
obs0.2211 134956 94.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15039 0 236 504 15779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d21.08
X-RAY DIFFRACTIONc_bond_d0.011

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