[English] 日本語
Yorodumi
- PDB-1hdc: MECHANISM OF INHIBITION OF 3ALPHA,20BETA-HYDROXYSTEROID DEHYDROGE... -

+
Open data


ID or keywords:

Loading...

-
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 (NAD+) 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more