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Yorodumi- PDB-3g1r: Crystal structure of human liver 5beta-reductase (AKR1D1) in comp... -
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-Basic information
Entry | Database: PDB / ID: 3g1r | ||||||
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Title | Crystal structure of human liver 5beta-reductase (AKR1D1) in complex with NADP and Finasteride. Resolution 1.70 A | ||||||
Components | 3-oxo-5-beta-steroid 4-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / FINASTERIDE complex / Bile acid catabolism / Cytoplasm / Disease mutation / Intrahepatic cholestasis / Lipid metabolism / NADP / Steroid metabolism | ||||||
Function / homology | Function and homology information Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid catabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / aldo-keto reductase (NADPH) activity / aldose reductase (NADPH) activity ...Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid catabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / aldo-keto reductase (NADPH) activity / aldose reductase (NADPH) activity / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cholesterol catabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / steroid binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.701 Å | ||||||
Authors | Di Costanzo, L. / Drury, J.E. / Penning, T.M. / Christianson, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Inhibition of human steroid 5beta-reductase (AKR1D1) by finasteride and structure of the enzyme-inhibitor complex. Authors: Drury, J.E. / Di Costanzo, L. / Penning, T.M. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g1r.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g1r.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/3g1r ftp://data.pdbj.org/pub/pdb/validation_reports/g1/3g1r | HTTPS FTP |
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-Related structure data
Related structure data | 3cmfS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 39599.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase #2: Chemical | #3: Chemical | ChemComp-FIT / ( | #4: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.4 Details: The ternary complexes of AKR1D1-NADP+-finasteride was crystallized by the hanging drop vapor diffusion method at 4 C. Drops containing 3.0 L of enzyme solution [5.0 mg/mL AKR1D1, 2.0 mM ...Details: The ternary complexes of AKR1D1-NADP+-finasteride was crystallized by the hanging drop vapor diffusion method at 4 C. Drops containing 3.0 L of enzyme solution [5.0 mg/mL AKR1D1, 2.0 mM NADP+, 0.5 mM finasteride, 10.0 mM Tris (pH 7.4)] and 4.0 L of precipitant buffer [0.1 M TRIS-HCl (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% iso-propanol] were equilibrated against a 1 mL reservoir of precipitant buffer. Crystals of the AKR1D1-NADP+-finasteride, complex were soaked for 24 hours in the same mother liquor solution augmented with 2.0 mm NADP+, 2.0 mM finasteride and 30% iso-propanol, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 76941 / Num. obs: 76941 / % possible obs: 97.8 % / Redundancy: 5 % / Biso Wilson estimate: 14.49 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.35 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3CMF Resolution: 1.701→24.337 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 19.22 / Stereochemistry target values: ML Details: The binding steroid pocket of monomer A showed a discontinuous peak that was not possible to fit with finasteride molecule or a different ligand.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.45 Å2 / ksol: 0.327 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.59 Å2 / Biso mean: 18.375 Å2 / Biso min: 5.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.701→24.337 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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