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Yorodumi- PDB-6udm: Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6udm | ||||||
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Title | Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) ICT-2726 | ||||||
Components | Cytochrome P450 1A1 | ||||||
Keywords | OXIDOREDUCTASE / CYP1A1 / P450 / Duocarmycin | ||||||
Function / homology | Function and homology information arachidonic acid monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / oxidoreductase activity, acting on diphenols and related substances as donors / long-chain fatty acid omega-1 hydroxylase activity / 9-cis-retinoic acid biosynthetic process / hydroperoxy icosatetraenoate dehydratase ...arachidonic acid monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / oxidoreductase activity, acting on diphenols and related substances as donors / long-chain fatty acid omega-1 hydroxylase activity / 9-cis-retinoic acid biosynthetic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / steroid 17-alpha-monooxygenase activity / : / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / coumarin metabolic process / response to 3-methylcholanthrene / maternal process involved in parturition / flavonoid metabolic process / porphyrin-containing compound metabolic process / response to iron(III) ion / hormone biosynthetic process / long-chain fatty acid metabolic process / Biosynthesis of protectins / epoxygenase P450 pathway / tissue remodeling / response to nematode / vitamin D 24-hydroxylase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / demethylase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / progesterone metabolic process / vitamin D metabolic process / hepatocyte differentiation / steroid biosynthetic process / Xenobiotics / amine metabolic process / response to arsenic-containing substance / camera-type eye development / digestive tract development / response to vitamin A / hydrogen peroxide biosynthetic process / long-chain fatty acid biosynthetic process / response to herbicide / estrogen metabolic process / retinol metabolic process / response to food / unspecific monooxygenase / aromatase activity / nitric oxide metabolic process / steroid metabolic process / cellular response to organic cyclic compound / response to immobilization stress / response to hyperoxia / positive regulation of G1/S transition of mitotic cell cycle / cellular response to copper ion / Hsp70 protein binding / monooxygenase activity / xenobiotic metabolic process / fatty acid metabolic process / Hsp90 protein binding / PPARA activates gene expression / oxygen binding / response to lipopolysaccharide / mitochondrial inner membrane / oxidoreductase activity / response to hypoxia / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.075 Å | ||||||
Authors | Bart, A.G. / Scott, E.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6udm.cif.gz | 706.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6udm.ent.gz | 593.4 KB | Display | PDB format |
PDBx/mmJSON format | 6udm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6udm_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6udm_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6udm_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 6udm_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6udm ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6udm | HTTPS FTP |
-Related structure data
Related structure data | 6udlC 4i8vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | 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: Homo sapiens (human) References: UniProt: P04798, unspecific monooxygenase, hydroperoxy icosatetraenoate dehydratase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-Q4P / [( #4: Chemical | ChemComp-CPS / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.58 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.16 M sodium phosphate dibasic, 16% w/v PEG3350, 1.8 mM n-decyl-B-D-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018 | |||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3.07→39.64 Å / Num. obs: 77258 / % possible obs: 99 % / Redundancy: 10.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.054 / Rrim(I) all: 0.173 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4I8V Resolution: 3.075→39.64 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 181.35 Å2 / Biso mean: 88.3601 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.075→39.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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