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- PDB-7qq7: Crystal structure of CYP142 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7qq7
TitleCrystal structure of CYP142 from Mycobacterium tuberculosis in complex with an inhibitor at partial occupancy with PEG
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / Cytochrome / P450 / Inhibitor / tuberculosis / cholesterol / 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
ACETATE ION / BROMIDE ION / Chem-EIQ / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSnee, M. / Levy, C. / Kavanagh, M.
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
DepositionJan 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: 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)45,87610
Polymers44,3711
Non-polymers1,5059
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-42 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.308, 65.191, 128.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Details (production host): Pet21 / 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 , 7 types, 473 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EIQ / ~{N}-[4-(pyridin-4-ylmethyl)phenyl]benzenesulfonamide


Mass: 324.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 8% PEG 20000, 8% PEG 550MME, 0.1M sodium acetate pH4.5, 0.2M KBr
Temp details: 4C

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 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: 1.6→55.31 Å / Num. obs: 62174 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.041 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3085 / CC1/2: 0.841 / Rrim(I) all: 0.864 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKR

2xkr


Resolution: 1.6→50.8 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1833 3176 5.12 %
Rwork0.1642 58909 -
obs0.1652 62085 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 88 464 3647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093446
X-RAY DIFFRACTIONf_angle_d1.0724709
X-RAY DIFFRACTIONf_chiral_restr0.0573511
X-RAY DIFFRACTIONf_plane_restr0.0131627
X-RAY DIFFRACTIONf_dihedral_angle_d14.30931354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.25941460.25582553X-RAY DIFFRACTION99.93
1.62-1.650.27811190.24932525X-RAY DIFFRACTION99.96
1.65-1.680.2281280.22592556X-RAY DIFFRACTION99.89
1.68-1.710.23981270.22232493X-RAY DIFFRACTION100
1.71-1.740.22681420.20552543X-RAY DIFFRACTION99.96
1.74-1.770.23731380.19882523X-RAY DIFFRACTION99.96
1.77-1.810.25221230.19142528X-RAY DIFFRACTION99.92
1.81-1.850.19921380.18312554X-RAY DIFFRACTION100
1.85-1.890.21011490.18552509X-RAY DIFFRACTION99.96
1.89-1.940.24421280.18622534X-RAY DIFFRACTION100
1.94-1.990.22621480.19092541X-RAY DIFFRACTION100
1.99-2.050.20731290.17562543X-RAY DIFFRACTION99.96
2.05-2.110.1891550.16152542X-RAY DIFFRACTION100
2.11-2.190.17141270.14692561X-RAY DIFFRACTION100
2.19-2.280.15771300.1482538X-RAY DIFFRACTION100
2.28-2.380.17481490.14572556X-RAY DIFFRACTION99.93
2.38-2.50.17531340.14332563X-RAY DIFFRACTION100
2.5-2.660.17881530.15172565X-RAY DIFFRACTION100
2.66-2.870.16571420.15092566X-RAY DIFFRACTION100
2.87-3.150.19061320.16432601X-RAY DIFFRACTION100
3.15-3.610.17121280.15532615X-RAY DIFFRACTION100
3.61-4.550.13981530.13192640X-RAY DIFFRACTION100
4.55-50.80.19051580.18492760X-RAY DIFFRACTION100

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