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- PDB-6udl: Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (... -

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Basic information

Entry
Database: PDB / ID: 6udl
TitleStructure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) ICT-2700
ComponentsCytochrome P450 1A1
KeywordsOXIDOREDUCTASE / CYP1A1 / P450 / Duocarmycin
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 / oxidoreductase activity, acting on diphenols and related substances as donors / response to Aroclor 1254 / phenol-containing compound metabolic process ...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 / oxidoreductase activity, acting on diphenols and related substances as donors / response to Aroclor 1254 / phenol-containing compound metabolic process / 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 / unspecific monooxygenase / response to herbicide / long-chain fatty acid biosynthetic process / 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 / monooxygenase activity / PPARA activates gene expression / fatty acid metabolic process / 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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-Q4M / Cytochrome P450 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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: 2021
Title: Cytochrome P450 binding and bioactivation of tumor-targeted duocarmycin agents
Authors: Bart, A.G. / Morais, G. / Vangala, V.R. / Loadman, P.M. / Pors, K. / Scott, E.E.
History
DepositionSep 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)227,00210
Polymers223,7774
Non-polymers3,2266
Water181
1
A: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9403
Polymers55,9441
Non-polymers9962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9403
Polymers55,9441
Non-polymers9962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
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
Unit cell
Length a, b, c (Å)65.371, 196.147, 237.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Cytochrome P450 1A1 / CYPIA1 / Cytochrome P450 form 6 / Cytochrome P450-C / Cytochrome P450-P1 / Hydroperoxy ...CYPIA1 / Cytochrome P450 form 6 / Cytochrome P450-C / Cytochrome P450-P1 / Hydroperoxy icosatetraenoate dehydratase


Mass: 55944.156 Da / Num. of mol.: 4 / Fragment: UNP 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, hydroperoxy icosatetraenoate dehydratase
#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-Q4M / [(1S)-1-(chloromethyl)-1,6-dihydropyrrolo[3,2-e]indol-3(2H)-yl](5-methoxy-1H-indol-2-yl)methanone


Mass: 379.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H18ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.18 M sodium phosphate dibasic, 18% PEG3350, 5 mM (S)-O-methyl-serine dodecylamide hydrochloride

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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
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 72081 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 67.44 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 28
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3422 / CC1/2: 0.322 / Rpim(I) all: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4I8V

4i8v


Resolution: 2.85→48.799 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2867 1990 2.78 %
Rwork0.2378 69719 -
obs0.2391 71709 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.51 Å2 / Biso mean: 75.1579 Å2 / Biso min: 31.76 Å2
Refinement stepCycle: final / Resolution: 2.85→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15015 0 382 1 15398
Biso mean--57.18 49.31 -
Num. residues----1877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.85-2.92120.33581220.3348438890
2.9212-3.00020.31321410.3288492599
3.0002-3.08840.38481420.32374943100
3.0884-3.18810.31151410.31414961100
3.1881-3.3020.37651430.29594969100
3.302-3.43420.33281420.2864984100
3.4342-3.59050.34361420.2724976100
3.5905-3.77970.33161420.25664985100
3.7797-4.01640.27851440.22865005100
4.0164-4.32630.27161430.21925037100
4.3263-4.76140.2461440.1995027100
4.7614-5.44960.27241460.20445090100
5.4496-6.86280.28691450.2445104100
6.8628-48.7990.23271530.1889532599

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