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- PDB-7p5t: Structure of CYP142 from Mycobacterium tuberculosis in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7p5t
TitleStructure of CYP142 from Mycobacterium tuberculosis in complex with inhibitor MEK216
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / tuberculosis / cholesterol / inhibitor / TB / heme / monooxygenase
Function / homology
Function and homology information


cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / peptidoglycan-based cell wall / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-5YG / BROMIDE ION / PROTOPORPHYRIN IX CONTAINING FE / : / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSnee, M. / Kavanagh, M. / Tunnicliffe, R. / McLean, K. / Levy, C. / Munro, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Fragment-Based Development of Small Molecule Inhibitors Targeting Mycobacterium tuberculosis Cholesterol Metabolism.
Authors: Kavanagh, M.E. / McLean, K.J. / Gilbert, S.H. / Amadi, C.N. / Snee, M. / Tunnicliffe, R.B. / Arora, K. / Boshoff, H.I.M. / Fanourakis, A. / Rebollo-Lopez, M.J. / Ortega, F. / Levy, C.W. / ...Authors: Kavanagh, M.E. / McLean, K.J. / Gilbert, S.H. / Amadi, C.N. / Snee, M. / Tunnicliffe, R.B. / Arora, K. / Boshoff, H.I.M. / Fanourakis, A. / Rebollo-Lopez, M.J. / Ortega, F. / Levy, C.W. / Munro, A.W. / Leys, D. / Abell, C. / Coyne, A.G.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 30, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6108
Polymers44,3711
Non-polymers1,2397
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-28 kcal/mol
Surface area15950 Å2
Unit cell
Length a, b, c (Å)55.728, 65.717, 129.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Steroid C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4- ...Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / Cholesterol C26-monooxygenase / Cholesterol C26-monooxygenase [(25R)-3beta-hydroxycholest-5-en-26-oate forming] / Cytochrome P450 142 / Steroid C27-monooxygenase


Mass: 44371.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WPL5, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-5YG / ~{N}-[(4-methoxyphenyl)methyl]-4-(pyridin-4-ylmethyl)aniline


Mass: 304.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.662 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 8% PEG 20,000, 8% PEG 550 MME, sodium acetate pH4.5, 0.1M potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→65.72 Å / Num. obs: 116304 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 1 / Rrim(I) all: 0.057 / Net I/σ(I): 11.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5347 / CC1/2: 0.566 / Rpim(I) all: 0.545 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKR

2xkr


Resolution: 1.3→64.53 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1617 5769 4.97 %
Rwork0.1367 110413 -
obs0.138 116182 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.64 Å2 / Biso mean: 25.4554 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: final / Resolution: 1.3→64.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 71 593 3755
Biso mean--18.33 42.8 -
Num. residues----396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.310.36281660.34283394356091
1.31-1.330.32781990.30273400359993
1.33-1.350.28071760.27213551372797
1.35-1.360.26241810.24123650383198
1.36-1.380.23822120.21533588380099
1.38-1.40.23421740.19463642381699
1.4-1.420.18681920.174136523844100
1.42-1.440.21842120.16273622383499
1.44-1.460.19651750.146937283903100
1.46-1.490.17991820.131236473829100
1.49-1.510.16711890.12736973886100
1.51-1.540.16131810.129837023883100
1.54-1.570.16911960.130736543850100
1.57-1.60.16182080.132137013909100
1.6-1.640.17571790.140336963875100
1.64-1.680.18562090.143136493858100
1.68-1.720.18481820.153237033885100
1.72-1.760.15922110.140736863897100
1.76-1.820.17041780.129736913869100
1.82-1.870.1431930.121337503943100
1.87-1.940.16761780.121136883866100
1.94-2.020.16982050.123437013906100
2.02-2.110.16272030.129437093912100
2.11-2.220.14022000.128437363936100
2.22-2.360.14991820.118137223904100
2.36-2.540.15252090.123837613970100
2.54-2.80.16132000.131837523952100
2.8-3.210.15222050.135137723977100
3.21-4.040.14611820.124638384020100
4.04-64.530.14382100.13863931414198

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