[English] 日本語
Yorodumi
- PDB-6o5y: Structure of Human Cytochrome P450 1A1 with 5-amino-N-(5-((4R,5R)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o5y
TitleStructure of Human Cytochrome P450 1A1 with 5-amino-N-(5-((4R,5R)-4-amino-5-fluoroazepan-1-yl)-1-methyl-1H-pyrazol-4-yl)-2-(2,6-difluorophenyl)thiazole-4-carboxamide)
ComponentsCytochrome P450 1A1
KeywordsOXIDOREDUCTASE / CYP1A1 / P450 / GDC-0339
Function / homology
Function and homology information


arachidonate monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / response to diphenyl ether / phenol-containing compound metabolic process / oxidoreductase activity, acting on diphenols and related substances as donors / response to Aroclor 1254 ...arachidonate monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / response to diphenyl ether / phenol-containing compound metabolic process / oxidoreductase activity, acting on diphenols and related substances as donors / response to Aroclor 1254 / long-chain fatty acid omega-1 hydroxylase activity / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / 9-cis-retinoic acid biosynthetic process / omega-hydroxylase P450 pathway / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / coumarin metabolic process / response to 3-methylcholanthrene / flavonoid metabolic process / porphyrin-containing compound metabolic process / maternal process involved in parturition / response to iron(III) ion / long-chain fatty acid metabolic process / Biosynthesis of protectins / epoxygenase P450 pathway / tissue remodeling / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / vitamin D 24-hydroxylase activity / lipid hydroxylation / demethylase activity / estrogen 16-alpha-hydroxylase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / vitamin D metabolic process / estrogen 2-hydroxylase activity / steroid biosynthetic process / hepatocyte differentiation / amine metabolic process / Xenobiotics / camera-type eye development / response to arsenic-containing substance / response to nematode / hydrogen peroxide biosynthetic process / digestive tract development / long-chain fatty acid biosynthetic process / response to vitamin A / response to herbicide / retinol metabolic process / estrogen metabolic process / unspecific monooxygenase / response to food / steroid metabolic process / : / response to immobilization stress / response to hyperoxia / positive regulation of G1/S transition of mitotic cell cycle / nitric oxide metabolic process / cellular response to copper ion / Hsp70 protein binding / xenobiotic metabolic process / fatty acid metabolic process / Hsp90 protein binding / monooxygenase activity / PPARA activates gene expression / oxygen binding / response to lipopolysaccharide / response to hypoxia / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / mitochondrion
Similarity search - Function
Cytochrome P450, E-class, group I, CYP1 / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-KUV / NITRATE ION / Cytochrome P450 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsBart, A.G. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM076343 United States
CitationJournal: Drug Metab.Dispos. / Year: 2020
Title: Human Cytochrome P450 1A1 Adapts Active Site for Atypical Nonplanar Substrate.
Authors: Bart, A.G. / Takahashi, R.H. / Wang, X. / Scott, E.E.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 1A1
B: Cytochrome P450 1A1
C: Cytochrome P450 1A1
D: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,77010
Polymers223,7774
Non-polymers2,9936
Water18010
1
A: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0263
Polymers55,9441
Non-polymers1,0822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6233
Polymers55,9441
Non-polymers6782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5612
Polymers55,9441
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5612
Polymers55,9441
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.147, 195.897, 236.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Cytochrome P450 1A1 / CYPIA1 / Cytochrome P450 form 6 / Cytochrome P450-C / Cytochrome P450-P1


Mass: 55944.156 Da / Num. of mol.: 4 / Fragment: residues 35-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP1A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04798, 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-KUV / 5-amino-N-{5-[(4R,5R)-4-amino-5-fluoroazepan-1-yl]-1-methyl-1H-pyrazol-4-yl}-2-(2,6-difluorophenyl)-1,3-thiazole-4-carboxamide


Mass: 465.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22F3N7OS
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium phosphate dibasic, 20% PEG3350, 10% glycerol, 1 mM hexadecyltrimethylammonium bromide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.16→50 Å / Num. obs: 52336 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.991 / Rpim(I) all: 0.102 / Net I/σ(I): 16.5
Reflection shellResolution: 3.16→3.21 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2539 / CC1/2: 0.49 / Rpim(I) all: 0.786 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DWM

6dwm


Resolution: 3.17→49.32 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.16
RfactorNum. reflection% reflection
Rfree0.2667 1999 3.83 %
Rwork0.2395 --
obs0.2405 52207 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.17→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15090 0 36 10 15136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515530
X-RAY DIFFRACTIONf_angle_d0.70621097
X-RAY DIFFRACTIONf_dihedral_angle_d4.1189196
X-RAY DIFFRACTIONf_chiral_restr0.0412277
X-RAY DIFFRACTIONf_plane_restr0.0052696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1679-3.24710.39461330.38813311X-RAY DIFFRACTION93
3.2471-3.33490.37671380.35353496X-RAY DIFFRACTION99
3.3349-3.4330.40171420.33593574X-RAY DIFFRACTION100
3.433-3.54370.32961410.32743531X-RAY DIFFRACTION100
3.5437-3.67040.35021420.31293592X-RAY DIFFRACTION100
3.6704-3.81730.30311430.29143572X-RAY DIFFRACTION100
3.8173-3.99090.28391420.26023569X-RAY DIFFRACTION100
3.9909-4.20120.25931420.24243576X-RAY DIFFRACTION100
4.2012-4.46430.24091440.22273604X-RAY DIFFRACTION100
4.4643-4.80870.23021420.21383598X-RAY DIFFRACTION100
4.8087-5.29210.21221450.21463619X-RAY DIFFRACTION100
5.2921-6.05670.2651440.22613648X-RAY DIFFRACTION100
6.0567-7.62630.25911470.22743687X-RAY DIFFRACTION100
7.6263-49.32750.21181540.16313831X-RAY DIFFRACTION99

+
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