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- PDB-1hdc: MECHANISM OF INHIBITION OF 3ALPHA,20BETA-HYDROXYSTEROID DEHYDROGE... -

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Basic information

Entry
Database: PDB / ID: 1hdc
TitleMECHANISM OF INHIBITION OF 3ALPHA,20BETA-HYDROXYSTEROID DEHYDROGENASE BY A LICORICE-DERIVED STEROIDAL INHIBITOR
Components3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


C21-steroid hormone metabolic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity
Similarity search - Function
short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBENOXOLONE / 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGhosh, D.
Citation
Journal: Structure / Year: 1994
Title: Mechanism of inhibition of 3 alpha, 20 beta-hydroxysteroid dehydrogenase by a licorice-derived steroidal inhibitor.
Authors: Ghosh, D. / Erman, M. / Wawrzak, Z. / Duax, W.L. / Pangborn, W.
#1: Journal: J.Steroid Biochem.Mol.Biol. / Year: 1992
Title: Inhibition of Streptomyces Hydrogenans 3Alpha,20Beta-Hydroxysteroid Dehydrogenase by Licorice-Derived Compounds and Crystallization of an Enzyme-Cofactor-Inhibitor Complex
Authors: Ghosh, D. / Erman, M. / Pangborn, W. / Duax, W.L. / Baker, M.E.
History
DepositionOct 21, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
B: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
C: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
D: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8468
Polymers105,5634
Non-polymers2,2834
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-147 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.050, 60.040, 59.840
Angle α, β, γ (deg.)101.78, 104.41, 96.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 26390.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria)
References: UniProt: P19992, 3alpha(or 20beta)-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-CBO / CARBENOXOLONE / Carbenoxolone


Mass: 570.757 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H50O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 261.1306-1308 1986
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.40-1.60 Mphosphate1reservoir
213-15 mg/mlprotein1drop
30.7 Mphosphate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 51.08 Å / Num. obs: 34405 / % possible obs: 71 % / Num. measured all: 48972 / Rmerge F obs: 0.114
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 65 %

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Processing

RefinementRfactor Rwork: 0.194 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 164 26 7558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.8
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 30996 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d1.8
X-RAY DIFFRACTIONo_dihedral_angle_d24.9
X-RAY DIFFRACTIONo_dihedral_angle_deg1.65

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