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- PDB-3na1: Crystal structure of human CYP11A1 in complex with 20-hydroxychol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3na1 | ||||||
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Title | Crystal structure of human CYP11A1 in complex with 20-hydroxycholesterol | ||||||
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![]() | Oxidoreductase / Electron transport / cytochrome P450 / 20-hydroxycholesterol / cholesterol side chain cleavage / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() cholesterol monooxygenase (side-chain-cleaving) / cholesterol monooxygenase (side-chain-cleaving) activity / Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / cortisol metabolic process / glucocorticoid biosynthetic process / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / sterol metabolic process ...cholesterol monooxygenase (side-chain-cleaving) / cholesterol monooxygenase (side-chain-cleaving) activity / Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / cortisol metabolic process / glucocorticoid biosynthetic process / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / sterol metabolic process / vitamin D metabolic process / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / steroid biosynthetic process / cellular response to peptide hormone stimulus / Endogenous sterols / cellular response to cAMP / cellular response to forskolin / cholesterol metabolic process / electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / iron ion binding / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Strushkevich, N.V. / MacKenzie, F. / Tempel, W. / Botchkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J.U. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system. Authors: Strushkevich, N. / Mackenzie, F. / Cherkesova, T. / Grabovec, I. / Usanov, S. / Park, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.2 KB | Display | ![]() |
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PDB format | ![]() | 180.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 60.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n9ySC ![]() 3n9zC ![]() 3na0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 56885.066 Da / Num. of mol.: 2 / Fragment: UNP residues 41-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P05108, cholesterol monooxygenase (side-chain-cleaving) #2: Protein | Mass: 13488.032 Da / Num. of mol.: 2 / Fragment: UNP residues 62-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 537 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/HCD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HCD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, Ca acetate, pH 7.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Date: Nov 18, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 74265 / % possible obs: 99.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.072 / Χ2: 1.987 / Net I/σ(I): 15.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3N9Y Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.887 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.59 Å2 / Biso mean: 25.989 Å2 / Biso min: 6.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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