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- PDB-6o5y: Structure of Human Cytochrome P450 1A1 with 5-amino-N-(5-((4R,5R)... -

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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) / demethylase activity / coumarin metabolic process / response to iron(III) ion / response to 3-methylcholanthrene / porphyrin-containing compound metabolic process / maternal process involved in parturition / flavonoid metabolic process / 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 / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / estrogen 2-hydroxylase activity / vitamin D metabolic process / steroid biosynthetic process / hepatocyte differentiation / amine metabolic process / Xenobiotics / response to arsenic-containing substance / camera-type eye development / response to nematode / response to vitamin A / hydrogen peroxide biosynthetic process / digestive tract development / retinol metabolic process / estrogen metabolic process / response to herbicide / long-chain fatty acid biosynthetic 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 / Hsp70 protein binding / xenobiotic metabolic process / cellular response to copper ion / Hsp90 protein binding / fatty acid metabolic process / monooxygenase activity / PPARA activates gene expression / oxygen binding / response to lipopolysaccharide / response to hypoxia / oxidoreductase activity / mitochondrial inner membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 3.36 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

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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

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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

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