[English] 日本語
Yorodumi
- PDB-3qu8: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qu8
TitleCrystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with the inhibitor 4-(4-Nitrobenzyl)pyridine.
ComponentsCytochrome P450 2B6
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / P450 / CYTOCHROME P450 2B6 / MONOOXYGENASE / MEMBRANE PROTEIN / CYP2B6 / ENDOPLASMIC RETICULUM / HEME / IRON / MEMBRANE / METAL BINDING / MICROSOME / PHOSPHOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / 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 / ketone metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity ...testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / 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 / ketone metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / epoxygenase P450 pathway / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / estrogen 2-hydroxylase activity / Xenobiotics / Phase I - Functionalization of compounds / 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 / xenobiotic catabolic process / 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, CYP2B-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, CYP2B-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
4-(4-nitrobenzyl)pyridine / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShah, M.B. / Pascual, J. / Stout, C.D. / Halpert, J.R.
CitationJournal: Mol.Pharmacol. / Year: 2011
Title: Structures of Cytochrome P450 2B6 Bound to 4-Benzylpyridine and 4-(4-Nitrobenzyl)pyridine: Insight into Inhibitor Binding and Rearrangement of Active Site Side Chains.
Authors: Shah, M.B. / Pascual, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Sep 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_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_label_asym_id / _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.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
Remark 999THE RESIDUES 3-21 (LSVLLFLALLTGLLLLLVQ) OF CORRESPONDING DATABASE REFERENCE SEQUENCE (UNP P20813) ...THE RESIDUES 3-21 (LSVLLFLALLTGLLLLLVQ) OF CORRESPONDING DATABASE REFERENCE SEQUENCE (UNP P20813) IS DELETED IN THIS STRUCTURE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 2B6
B: Cytochrome P450 2B6
C: Cytochrome P450 2B6
D: Cytochrome P450 2B6
E: Cytochrome P450 2B6
F: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,60325
Polymers327,8766
Non-polymers8,72719
Water2,702150
1
A: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9714
Polymers54,6461
Non-polymers1,3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4665
Polymers54,6461
Non-polymers1,8204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9714
Polymers54,6461
Non-polymers1,3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4665
Polymers54,6461
Non-polymers1,8204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9714
Polymers54,6461
Non-polymers1,3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7573
Polymers54,6461
Non-polymers1,1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.880, 101.880, 299.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A28 - 492
2112B28 - 492
3112C28 - 492
4112D28 - 492
5112E28 - 492
6112F28 - 492

-
Components

#1: Protein
Cytochrome P450 2B6


Mass: 54646.004 Da / Num. of mol.: 6 / Fragment: Cytochrome P450 2B6, residues 3-21 deleted
Mutation: E2A, R22K, H23K, P24T, N25S, T26S, H27K, D28G, R29K, Y226H, K262R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P20813, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-3QU / 4-(4-nitrobenzyl)pyridine


Mass: 214.220 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H10N2O2
#4: Chemical
ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 291 K / pH: 7
Details: 0.15 M DL-Malic Acid, 20 % w/v PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→84.6 Å / Num. obs: 76085 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 52.67 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.368 / % possible all: 78.6

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
BALBESphasing
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IBD

3ibd


Resolution: 2.8→50.51 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.814 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3815 5 %RANDOM
Rwork0.218 ---
obs0.22 72191 88.9 %-
all-81196 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22228 0 586 150 22964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02223471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7192.0231828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34552742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13522.8651089
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.436153892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.86715178
X-RAY DIFFRACTIONr_chiral_restr0.1220.23432
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117806
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_it0.6131.513760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24222291
X-RAY DIFFRACTIONr_scbond_it1.88439711
X-RAY DIFFRACTIONr_scangle_it3.3374.59537
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1792tight positional0.070.05
2B1792tight positional0.060.05
3C1792tight positional0.070.05
4D1792tight positional0.060.05
5E1792tight positional0.060.05
6F1792tight positional0.070.05
1A1818medium positional0.090.5
2B1818medium positional0.070.5
3C1818medium positional0.070.5
4D1818medium positional0.070.5
5E1818medium positional0.080.5
6F1818medium positional0.080.5
1A1792tight thermal0.130.5
2B1792tight thermal0.130.5
3C1792tight thermal0.140.5
4D1792tight thermal0.120.5
5E1792tight thermal0.130.5
6F1792tight thermal0.210.5
1A1818medium thermal0.142
2B1818medium thermal0.142
3C1818medium thermal0.152
4D1818medium thermal0.132
5E1818medium thermal0.142
6F1818medium thermal0.212
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 242 -
Rwork0.305 4529 -
obs--75.97 %

+
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