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- PDB-6t0l: Crystal structure of CYP124 in complex with inhibitor compound 5' -

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Basic information

Entry
Database: PDB / ID: 6t0l
TitleCrystal structure of CYP124 in complex with inhibitor compound 5'
ComponentsCYP124 in complex with inhibitor compound 5'
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / CYP / CYP124 / 124 / inhibition / inhibitor / drug / antituberculosis / tuberculosis / mycobacterium tuberculosis / compound / 5'
Function / homology
Function and homology information


methyl-branched lipid omega-hydroxylase / methyl-branched fatty acid metabolic process / cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / fatty acid omega-oxidation / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / NADPH binding / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-M8N / DI(HYDROXYETHYL)ETHER / Methyl-branched lipid omega-hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBukhdruker, S. / Marin, E. / Varaksa, T. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-54-00030 Russian Federation
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis.
Authors: 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. ...Authors: 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.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Feb 17, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_nonpoly_scheme / struct_site_gen
Item: _atom_site.auth_seq_id / _citation.year ..._atom_site.auth_seq_id / _citation.year / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYP124 in complex with inhibitor compound 5'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3308
Polymers48,8691
Non-polymers1,4617
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-23 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.570, 71.570, 195.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYP124 in complex with inhibitor compound 5'


Mass: 48868.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP3

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Non-polymers , 7 types, 387 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-M8N / ~{N}-[[[2-methyl-4-(3-methylbutyl)phenyl]amino]methyl]hydroxylamine


Mass: 222.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 60287 / % possible obs: 98.7 % / Redundancy: 11.7 % / Biso Wilson estimate: 28.85 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.12 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
7.42-301248.67990.9990.04497.7
5.25-7.4211.24113570.9980.05399.9
4.29-5.2512.145.117070.9990.05100
3.71-4.2912.943.119800.9990.052100
3.32-3.7112.936.922290.9990.06100
3.03-3.3211.728.524440.9990.079100
2.81-3.0312.623.426300.9980.107100
2.62-2.8113.118.328210.9970.142100
2.47-2.6213.51529760.9960.183100
2.35-2.4713.712.231650.9940.232100
2.24-2.3512.79.332850.9930.29999.9
2.14-2.2412.2734690.9860.393100
2.06-2.1413.15.435710.9760.533100
1.98-2.0613.33.937040.9870.698100
1.92-1.9813.12.838700.9390.937100
1.86-1.9212.7239870.8991.232100
1.8-1.8611.81.540810.8141.58799.9
1.75-1.89.60.941480.6612.14899.2
1.7-1.757.50.740910.5142.67594.3
1.66-1.76.20.539730.4013.55789.4

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Processing

Software
NameVersionClassification
MxCuBE2data collection
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0F

6t0f


Resolution: 1.8→29.67 Å / SU ML: 0.1722 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0601
RfactorNum. reflection% reflection
Rfree0.1923 2404 5 %
Rwork0.1633 --
obs0.1648 48050 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 94 380 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093733
X-RAY DIFFRACTIONf_angle_d1.05455117
X-RAY DIFFRACTIONf_chiral_restr0.0602542
X-RAY DIFFRACTIONf_plane_restr0.0081682
X-RAY DIFFRACTIONf_dihedral_angle_d20.70051375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30371400.28662640X-RAY DIFFRACTION99.71
1.84-1.880.3161370.27252602X-RAY DIFFRACTION99.38
1.88-1.920.26981400.24982623X-RAY DIFFRACTION99.82
1.92-1.970.30291390.2262644X-RAY DIFFRACTION99.78
1.97-2.020.23671390.2062639X-RAY DIFFRACTION99.61
2.02-2.080.20511380.18662636X-RAY DIFFRACTION99.82
2.08-2.150.22561390.1782644X-RAY DIFFRACTION99.89
2.15-2.220.21171390.17332665X-RAY DIFFRACTION99.93
2.22-2.310.21561400.17592665X-RAY DIFFRACTION99.82
2.31-2.420.2251400.16862656X-RAY DIFFRACTION99.89
2.42-2.550.20861410.16632680X-RAY DIFFRACTION99.93
2.55-2.710.21691400.15892674X-RAY DIFFRACTION100
2.71-2.920.17691430.1582699X-RAY DIFFRACTION100
2.92-3.210.18611430.16012716X-RAY DIFFRACTION100
3.21-3.670.19631430.14892733X-RAY DIFFRACTION100
3.67-4.620.14161470.12572784X-RAY DIFFRACTION100
4.62-29.670.16971560.16182946X-RAY DIFFRACTION99.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69682929837-0.4519432775630.00022080616382.179712632770.3286856641192.369270902-0.1489319221670.1911530271230.118689396431-0.2192489105910.177482551788-0.236774050457-0.2589705153770.29642614022-0.018997845090.297352824886-0.0840991831580.003574363085710.293924555613-0.03041050299690.24469940826226.4945511962-0.39401990839247.4669922818
20.688601580874-0.00793026157012-0.03055262962580.9837106258150.4958243384761.57159477436-0.101931089587-0.01994528974350.01125996097840.06435818909230.136671823466-0.106107431293-0.1220208291980.298345571107-0.02480923887640.217707533937-0.0131525991571-0.02445795466460.216044585032-0.007987101315540.22589382555229.01106404773.6414317931266.0802880275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 428 )

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