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- PDB-8fda: Human Cytochrome P450 17A1 in complex with steroidal isonitrile i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fda | ||||||
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Title | Human Cytochrome P450 17A1 in complex with steroidal isonitrile inhibitor | ||||||
![]() | Steroid 17-alpha-hydroxylase/17,20 lyase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 17A1 / Cytochrome P450 c17 / 17-alpha hydroxylase / 17 / 20 lyase / isonitrile / steroid | ||||||
Function / homology | ![]() Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process ...Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process / sex differentiation / progesterone metabolic process / steroid biosynthetic process / steroid metabolic process / oxygen binding / iron ion binding / axon / neuronal cell body / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Richard, A.M. / Scott, E.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Selective steroidogenic cytochrome P450 haem iron ligation by steroid-derived isonitriles. Authors: Richard, A.M. / Wong, N.R. / Harris, K. / Sundar, R. / Scott, E.E. / Pochapsky, T.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 719.5 KB | Display | ![]() |
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PDB format | ![]() | 599.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 70.4 KB | Display | |
Data in CIF | ![]() | 92.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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: 55740.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P05093, steroid 17alpha-monooxygenase, 17alpha-hydroxyprogesterone deacetylase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-XPK / [( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl (pH 8.5), 0.25 M LiSO4, 30% PEG 3350, and 7% sucrose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2022 Details: Beam focused to 50 by 15 microns, beam attenuated 96.5% |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38.96 Å / Num. obs: 114766 / % possible obs: 99.6 % / Redundancy: 13.4 % / Biso Wilson estimate: 44.37 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.075 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 16489 / CC1/2: 0.382 / Rpim(I) all: 1.453 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.96 Å
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Refine LS restraints |
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LS refinement shell |
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