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- PDB-6csb: V308E mutant of cytochrome P450 2D6 complexed with thioridazine -

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Basic information

Entry
Database: PDB / ID: 6csb
TitleV308E mutant of cytochrome P450 2D6 complexed with thioridazine
ComponentsCytochrome P450 2D6CYP2D6
KeywordsOXIDOREDUCTASE / conformational change proximal surface distal surface substrate binding C-D loop
Function / homology
Function and homology information


negative regulation of binding / negative regulation of cellular organofluorine metabolic process / Miscellaneous substrates / isoquinoline alkaloid metabolic process / Fatty acids / 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 metabolic process / anandamide 8,9 epoxidase activity ...negative regulation of binding / negative regulation of cellular organofluorine metabolic process / Miscellaneous substrates / isoquinoline alkaloid metabolic process / Fatty acids / 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 metabolic process / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / alkaloid catabolic process / alkaloid metabolic process / : / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / Xenobiotics / oxidative demethylation / 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 / retinol metabolic process / Aspirin ADME / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / cholesterol metabolic process / monooxygenase activity / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2D-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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-RTZ / Cytochrome P450 2D6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsYang, Y.T. / Fujita, K. / Wang, P.F. / Im, S.C. / Pearl, N.M. / Meagher, J. / Stuckey, J. / Waskell, L.
CitationJournal: To Be Published
Title: Characteristic conformational changes on the distal and proximal surfaces of cytochrome P450 2D6 in response to substrate binding
Authors: Yang, Y.T. / Fujita, F. / Wang, P.F. / Im, S.C. / Pearl, N.M. / Meagher, J. / Stuckey, J. / Waskell, L.
History
DepositionMar 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Oct 4, 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
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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 2D6
B: Cytochrome P450 2D6
C: Cytochrome P450 2D6
D: Cytochrome P450 2D6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,35130
Polymers215,0424
Non-polymers7,30926
Water9,836546
1
A: Cytochrome P450 2D6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6948
Polymers53,7611
Non-polymers1,9337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2D6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7539
Polymers53,7611
Non-polymers1,9928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 2D6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7218
Polymers53,7611
Non-polymers1,9607
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 2D6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1845
Polymers53,7611
Non-polymers1,4234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.738, 191.999, 250.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome P450 2D6 / CYP2D6 / CYPIID6 / Cholesterol 25-hydroxylase / Cytochrome P450-DB1 / Debrisoquine 4-hydroxylase


Mass: 53760.551 Da / Num. of mol.: 4 / Fragment: residues 34-497 / Mutation: V308E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2D6, CYP2DL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10635, unspecific monooxygenase

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Non-polymers , 7 types, 572 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-RTZ / 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine


Mass: 370.575 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H26N2S2
#4: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: mixing 1.5 ul of the protein solution, 0.25 ul 70 mM HEGA-10, and 0.3 ul of the reservoir solution containing 10-20% of PEG 400, 0.1 M cacodylate, pH 7.0, 2 mM ZnSO4, and 200 mM MgAc2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.394→152.78 Å / Num. obs: 105941 / % possible obs: 95.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TBG

3tbg


Resolution: 2.394→48.47 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.94
RfactorNum. reflection% reflection
Rfree0.2292 5224 4.95 %
Rwork0.193 --
obs0.1948 105561 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.394→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14017 0 415 546 14978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814932
X-RAY DIFFRACTIONf_angle_d1.02420401
X-RAY DIFFRACTIONf_dihedral_angle_d7.86512200
X-RAY DIFFRACTIONf_chiral_restr0.0512218
X-RAY DIFFRACTIONf_plane_restr0.0072781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3941-2.42130.30511380.27442859X-RAY DIFFRACTION83
2.4213-2.44980.28291650.25673022X-RAY DIFFRACTION88
2.4498-2.47970.29681780.24133053X-RAY DIFFRACTION89
2.4797-2.5110.28191710.24583114X-RAY DIFFRACTION89
2.511-2.54410.26211570.23223101X-RAY DIFFRACTION90
2.5441-2.57890.26481620.2263105X-RAY DIFFRACTION90
2.5789-2.61580.28651950.22273128X-RAY DIFFRACTION90
2.6158-2.65480.26911490.21913177X-RAY DIFFRACTION91
2.6548-2.69630.23561530.21763199X-RAY DIFFRACTION92
2.6963-2.74050.27621610.21613246X-RAY DIFFRACTION92
2.7405-2.78780.28261740.2133240X-RAY DIFFRACTION94
2.7878-2.83840.25241600.22013265X-RAY DIFFRACTION94
2.8384-2.8930.31171680.22863378X-RAY DIFFRACTION95
2.893-2.95210.2671850.22423307X-RAY DIFFRACTION96
2.9521-3.01630.24461650.22543391X-RAY DIFFRACTION97
3.0163-3.08640.26531920.21593394X-RAY DIFFRACTION98
3.0864-3.16360.26461740.21213429X-RAY DIFFRACTION98
3.1636-3.24910.27181610.21523475X-RAY DIFFRACTION99
3.2491-3.34470.23361840.21273460X-RAY DIFFRACTION99
3.3447-3.45260.25572080.19973451X-RAY DIFFRACTION99
3.4526-3.5760.20851750.19243508X-RAY DIFFRACTION99
3.576-3.71910.23681670.18493486X-RAY DIFFRACTION100
3.7191-3.88830.20251660.1753550X-RAY DIFFRACTION100
3.8883-4.09320.19391810.15743540X-RAY DIFFRACTION100
4.0932-4.34950.17641910.15643518X-RAY DIFFRACTION100
4.3495-4.68510.16261960.14743530X-RAY DIFFRACTION100
4.6851-5.15610.22581780.15773592X-RAY DIFFRACTION100
5.1561-5.9010.26781790.19313604X-RAY DIFFRACTION100
5.901-7.43040.23711820.19823635X-RAY DIFFRACTION100
7.4304-48.47950.16642090.18073580X-RAY DIFFRACTION94

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