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- PDB-7zgl: Crystal structure of CYP125 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7zgl
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / CYP125 / P450 / Cholesterol / oxidase / inhibitor / complex / Cytochrome / tuberculosis / MTB / Mycobacterium / monooxygenase
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / biological process involved in interaction with host / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EIQ / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionApr 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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
B: Steroid C26-monooxygenase
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,96212
Polymers139,9903
Non-polymers2,9729
Water4,918273
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6755
Polymers46,6631
Non-polymers1,0124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6043
Polymers46,6631
Non-polymers9412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6824
Polymers46,6631
Non-polymers1,0193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.306, 69.329, 144.892
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Steroid C26-monooxygenase / Cholest-4-en-3-one 26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25S)-3-oxocholest-4-en- ...Cholest-4-en-3-one 26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / Cholesterol C26-monooxygenase / Cholesterol C26-monooxygenase [(25S)-3beta-hydroxycholest-5-en-26-oate forming] / Cytochrome P450 125 / Steroid C27-monooxygenase


Mass: 46663.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp125, cyp125A1, Rv3545c, MTCY03C7.11 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WPP1, cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 5 types, 282 molecules

#2: Chemical ChemComp-EIQ / ~{N}-[4-(pyridin-4-ylmethyl)phenyl]benzenesulfonamide


Mass: 324.397 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1M MES pH 6.2, 1.9M ammonium sulphate / Temp details: 4C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.5→144.46 Å / Num. obs: 46975 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.95 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.096 / Net I/σ(I): 4.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4600 / CC1/2: 0.599 / Rpim(I) all: 0.593 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XN8

2xn8


Resolution: 2.5→144.46 Å / SU ML: 0.3437 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 2344 5 %
Rwork0.2103 44526 -
obs0.2124 46870 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→144.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9654 0 204 273 10131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004410154
X-RAY DIFFRACTIONf_angle_d0.650613818
X-RAY DIFFRACTIONf_chiral_restr0.04191412
X-RAY DIFFRACTIONf_plane_restr0.00481832
X-RAY DIFFRACTIONf_dihedral_angle_d16.93333738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.38631330.32212627X-RAY DIFFRACTION99.35
2.55-2.610.35651530.29482538X-RAY DIFFRACTION99.89
2.61-2.670.30891580.2752603X-RAY DIFFRACTION99.75
2.67-2.730.33491360.25872627X-RAY DIFFRACTION99.89
2.73-2.810.25451230.2522594X-RAY DIFFRACTION99.89
2.81-2.890.30621240.26252620X-RAY DIFFRACTION99.82
2.89-2.980.33051570.26932576X-RAY DIFFRACTION99.78
2.98-3.090.31441340.25332631X-RAY DIFFRACTION99.93
3.09-3.210.26951220.2412594X-RAY DIFFRACTION99.6
3.21-3.360.23411370.23222624X-RAY DIFFRACTION99.42
3.36-3.540.28721430.2162605X-RAY DIFFRACTION99.78
3.54-3.760.27441270.22922616X-RAY DIFFRACTION99.35
3.76-4.050.25461300.18982637X-RAY DIFFRACTION99.71
4.05-4.460.21111540.16612616X-RAY DIFFRACTION99.89
4.46-5.10.20131370.16112633X-RAY DIFFRACTION99.86
5.1-6.430.23251410.20182650X-RAY DIFFRACTION99.5
6.43-144.460.16331350.15912735X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 29.7071267838 Å / Origin y: -4.58112441167 Å / Origin z: 37.8191397066 Å
111213212223313233
T0.363641706962 Å20.0248509702342 Å2-0.0327775042341 Å2-0.314321467823 Å20.0262144307536 Å2--0.335760471512 Å2
L0.170621086825 °2-0.071934995072 °2-0.427325188182 °2-0.420332030979 °20.205558392381 °2--1.2493904106 °2
S-0.0607590050808 Å °0.0156599812734 Å °-0.0440617835665 Å °-0.185631202329 Å °-0.0188264965098 Å °-0.0183370112474 Å °0.14656218434 Å °0.0986339485807 Å °0.0814255959362 Å °
Refinement TLS groupSelection details: all

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