[English] 日本語
Yorodumi
- PDB-3t3z: Human Cytochrome P450 2E1 in complex with pilocarpine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t3z
TitleHuman Cytochrome P450 2E1 in complex with pilocarpine
ComponentsCytochrome P450 2E1
KeywordsOXIDOREDUCTASE / CYP2E1 / cytochrome P450 2E1 / P450 2E1 / heme protein / monooxygenase / drug metabolism / xenobiotic metabolism / endoplasmic reticulum / membrane
Function / homology
Function and homology information


: / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / 4-nitrophenol 2-monooxygenase activity / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity ...: / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / 4-nitrophenol 2-monooxygenase activity / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / lipid hydroxylation / 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 / 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 / unspecific monooxygenase / long-chain fatty acid biosynthetic process / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / xenobiotic metabolic process / response to bacterium / Hsp90 protein binding / monooxygenase activity / oxygen binding / oxidoreductase activity / mitochondrial inner membrane / 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 ...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
sucrose / Chem-9PL / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMeneely, K.M. / DeVore, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 29, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 2E1
B: Cytochrome P450 2E1
C: Cytochrome P450 2E1
D: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,90216
Polymers220,2344
Non-polymers4,66812
Water12,863714
1
A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2264
Polymers55,0581
Non-polymers1,1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2264
Polymers55,0581
Non-polymers1,1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2264
Polymers55,0581
Non-polymers1,1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2264
Polymers55,0581
Non-polymers1,1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Cytochrome P450 2E1
hetero molecules

A: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4518
Polymers110,1172
Non-polymers2,3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4620 Å2
ΔGint-62 kcal/mol
Surface area38510 Å2
MethodPISA
6
B: Cytochrome P450 2E1
D: Cytochrome P450 2E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4518
Polymers110,1172
Non-polymers2,3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-60 kcal/mol
Surface area38550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.638, 100.638, 259.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein
Cytochrome P450 2E1 / 4-nitrophenol 2-hydroxylase / CYPIIE1 / Cytochrome P450-J


Mass: 55058.488 Da / Num. of mol.: 4 / Fragment: unp residues 31-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2E, CYP2E1 / Plasmid: pKK2E1dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3
References: UniProt: P05181, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: 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.: 4 / Source method: obtained synthetically / Formula: C11H16N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 8% PEG MME 2000, 12% isopropanol, and 0.1 M NaHEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.98
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2009
Details: SAGITALLY FOCUSED SECOND CRYSTAL, VERTICAL FOCUSING VIA A ONE-METER, PT/PD-COATED CYLINDRICALLY FOCUSING MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→37 Å / Num. obs: 102444 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.76 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 6.6
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.6 / % possible all: 84.3

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERMRphasing
REFMAC6.1.13refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→36.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.392 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28051 5103 5 %RANDOM
Rwork0.21735 ---
obs0.22049 97337 95.93 %-
all-97337 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.995 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.321 Å
Refinement stepCycle: LAST / Resolution: 2.35→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15148 0 324 714 16186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02215953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6292.01721681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13151858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42223.182751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.232152710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.12815116
X-RAY DIFFRACTIONr_chiral_restr0.1180.22307
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112184
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_it0.8571.59317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.544215178
X-RAY DIFFRACTIONr_scbond_it2.48536636
X-RAY DIFFRACTIONr_scangle_it3.7934.56500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 316 -
Rwork0.289 6193 -
obs--82.77 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more