8A6W | pdb_00008a6w

Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with cholestenone

• PDB DOI: https://doi.org/10.2210/pdb8A6W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-20 Released: 2023-07-05 
• Deposition Author(s): Snee, M., Amadi, C., Levy, C.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with cholestenone

Snee, M., Amadi, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 95.24 kDa 
• Atom Count: 6,824 
• Modeled Residue Count: 790 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid C26-monooxygenase	A [auth B], B [auth E]	418	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: cyp142, cyp142A1, Rv3518c, MTV023.25c EC: 1.14.15.28
UniProt
Find proteins for P9WPL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPL5  Go to UniProtKB:  P9WPL5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth B], F [auth E]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
K2B (Subject of Investigation/LOI)	C [auth B], E	(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE C27 H44 O NYOXRYYXRWJDKP-GYKMGIIDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K2B	BindingDB:  8A6W	Kd: 360 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.81	α = 90
b = 128.13	β = 90
c = 146.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Snee, M., Amadi, C., Levy, C.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description