6T0F | pdb_00006t0f

Crystal structure of CYP124 in complex with cholest-4-en-3-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6T0F

Ligand Structure Quality Assessment 


This is version 2.1 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 Biology 433: 166763-166763

  • DOI: https://doi.org/10.1016/j.jmb.2020.166763
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 202.32 kDa 
  • Atom Count: 18,282 
  • Modeled Residue Count: 1,722 
  • Deposited Residue Count: 1,740 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyl-branched lipid omega-hydroxylase
A, B, C, D
435Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: cyp124Rv2266MTCY339.44c
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
CA [auth D],
E [auth A],
N [auth B],
V [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
K2B
(Subject of Investigation/LOI)

Query on K2B



Download:Ideal Coordinates CCD File
DA [auth D],
F [auth A],
O [auth B],
W [auth C]
(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
C27 H44 O
NYOXRYYXRWJDKP-GYKMGIIDSA-N
MPO

Query on MPO



Download:Ideal Coordinates CCD File
EA [auth D],
G [auth A],
P [auth B],
X [auth C]
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
FA [auth D]
L [auth A]
T [auth B]
AA [auth C],
BA [auth C],
FA [auth D],
L [auth A],
T [auth B],
U [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
GA [auth D]
H [auth A]
HA [auth D]
I [auth A]
J [auth A]
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
J [auth A],
K [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.67α = 90
b = 81.27β = 107.286
c = 155.85γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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, Derived calculations
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description