6T0H

Crystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis.

Varaksa, T.Bukhdruker, S.Grabovec, I.Marin, E.Kavaleuski, A.Gusach, A.Kovalev, K.Maslov, I.Luginina, A.Zabelskii, D.Astashkin, R.Shevtsov, M.Smolskaya, S.Kavaleuskaya, A.Shabunya, P.Baranovsky, A.Dolgopalets, V.Charnou, Y.Savachka, A.Litvinovskaya, R.Hurski, A.Shevchenko, E.Rogachev, A.Mishin, A.Gordeliy, V.Gabrielian, A.Hurt, D.E.Nikonenko, B.Majorov, K.Apt, A.Rosenthal, A.Gilep, A.Borshchevskiy, V.Strushkevich, N.

(2021) J Mol Biol 433: 166763-166763

  • DOI: https://doi.org/10.1016/j.jmb.2020.166763
  • Primary Citation of Related Structures:  
    6T0F, 6T0G, 6T0H, 6T0K, 6T0L

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) infection is among top ten causes of death worldwide, and the number of drug-resistant strains is increasing. The direct interception of human immune signaling molecules by Mtb remains elusive, limiting drug discovery. Oxysterols and secosteroids regulate both innate and adaptive immune responses. Here we report a functional, structural, and bioinformatics study of Mtb enzymes initiating cholesterol catabolism and demonstrated their interrelation with human immunity. We show that these enzymes metabolize human immune oxysterol messengers. Rv2266 - the most potent among them - can also metabolize vitamin D3 (VD3) derivatives. High-resolution structures show common patterns of sterols binding and reveal a site for oxidative attack during catalysis. Finally, we designed a compound that binds and inhibits three studied proteins. The compound shows activity against Mtb H37Rv residing in macrophages. Our findings contribute to molecular understanding of suppression of immunity and suggest that Mtb has its own transformation system resembling the human phase I drug-metabolizing system.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYP124 in complex with inhibitor carbethoxyhexyl imidazole435Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 1.14.15.14 (PDB Primary Data), 1.14.15.28 (PDB Primary Data)
UniProt
Find proteins for P9WPP3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP3 
Go to UniProtKB:  P9WPP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
M9B (Subject of Investigation/LOI)
Query on M9B

Download Ideal Coordinates CCD File 
C [auth A]1-alpha-hydroxy-vitamin D3
C27 H44 O2
OFHCOWSQAMBJIW-AVJTYSNKSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth A]
J [auth A]
K [auth A]
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth A],
Q [auth A],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.56α = 90
b = 74.97β = 106.952
c = 56.63γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation18-54-00030

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2021-02-03
    Changes: Database references
  • Version 2.0: 2021-02-17
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2023-01-25
    Changes: Database references
  • Version 2.2: 2024-02-07
    Changes: Data collection, Refinement description