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- PDB-5a1p: Crystal structure of cytochrome P450 3A4 bound to progesterone an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a1p | ||||||
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Title | Crystal structure of cytochrome P450 3A4 bound to progesterone and citrate | ||||||
![]() | CYTOCHROME P450 3A4 | ||||||
![]() | OXIDOREDUCTASE / CYTOCHROME P450 3A4 / CYP3A4 / MONOOXYGENASE / PROGESTERONE / CITRATE | ||||||
Function / homology | ![]() quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / vitamin D metabolic process / Atorvastatin ADME / oxidative demethylation / : / steroid catabolic process / Xenobiotics / Phase I - Functionalization of compounds / long-chain fatty acid biosynthetic process / estrogen metabolic process / retinol metabolic process / retinoic acid metabolic process / Prednisone ADME / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / androgen metabolic process / steroid hydroxylase activity / xenobiotic catabolic process / monooxygenase activity / steroid binding / cholesterol metabolic process / xenobiotic metabolic process / lipid metabolic process / oxygen binding / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sevrioukova, I. / Poulos, T. | ||||||
![]() | ![]() Title: Anion-Dependent Stimulation of Cyp3A4 Monooxygenase. Authors: Sevrioukova, I.F. / Poulos, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.4 KB | Display | ![]() |
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PDB format | ![]() | 167.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a1rC ![]() 1tqnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 55757.812 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, 23-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P08684, EC: 1.14.13.157, EC: 1.14.13.32, EC: 1.14.13.67, kynurenine 3-monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-STR / |
#4: Chemical | ChemComp-CIT / |
#5: Water | ChemComp-HOH / |
Sequence details | RESIDUES 3-22 DELETED, C-TERMINAL HIS-TAG 504-507 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 6% PEG 3350, 20 MM BIS-TRIS PROPANE PH 6.4, 12 MM AMMONIUM CITRATE, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 2, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→65.85 Å / Num. obs: 16864 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 66.54 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TQN Resolution: 2.5→38.67 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 26.22 / Stereochemistry target values: ML Details: RESIDUES 2, 23-25,265-267,282-285,AND 498-507 ARE DISORDERED AND NOT SEEN IN THE CRYSTAL STRUCTURE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→38.67 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -19.2533 Å / Origin y: 23.7077 Å / Origin z: 12.5368 Å
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Refinement TLS group | Selection details: (CHAIN A AND RESSEQ -10:9999) |