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- PDB-6tev: The structure of CYP121 in complex with inhibitor L44 -

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Basic information

Entry
Database: PDB / ID: 6tev
TitleThe structure of CYP121 in complex with inhibitor L44
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / CYP121 / Inhibitor / Complex
Function / homology
Function and homology information


mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-N5W / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70001263917 Å
AuthorsAdam, S. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKO 4116/3-2 Germany
CitationJournal: Chemmedchem / Year: 2021
Title: Structure-Activity Relationship and Mode-Of-Action Studies Highlight 1-(4-Biphenylylmethyl)-1H-imidazole-Derived Small Molecules as Potent CYP121 Inhibitors.
Authors: Walter, I. / Adam, S. / Gentilini, M.V. / Kany, A.M. / Brengel, C. / Thomann, A. / Sparwasser, T. / Kohnke, J. / Hartmann, R.W.
History
DepositionNov 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6516
Polymers43,3061
Non-polymers1,3455
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-21 kcal/mol
Surface area16070 Å2
Unit cell
Length a, b, c (Å)77.555, 77.555, 264.188
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-1323-

HOH

21A-1324-

HOH

31A-1371-

HOH

41A-1435-

HOH

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Components

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, MT2336 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP6, mycocyclosin synthase
#2: Chemical ChemComp-N5W / 1-[[4-[4-(trifluoromethyl)phenyl]phenyl]methyl]imidazole


Mass: 302.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13F3N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Calcium acetate, sodium acetate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.09 Å / Num. obs: 52925 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.4888732536 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.79 Å / Num. unique obs: 7523 / CC1/2: 0.891 / Rpim(I) all: 0.227

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Processing

Software
NameVersionClassification
Coot0.8.9.1refinement
PHENIX1.11.1_2575refinement
pointlessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N40

1n40


Resolution: 1.70001263917→41.5275178694 Å / SU ML: 0.181072114174 / Cross valid method: FREE R-VALUE / σ(F): 1.33626287157 / Phase error: 17.6547622842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188569730996 2735 5.17717876883 %
Rwork0.17052265459 50093 -
obs0.171463540513 52828 99.9281201528 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.5468479361 Å2
Refinement stepCycle: LAST / Resolution: 1.70001263917→41.5275178694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 52 440 3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005311781169743180
X-RAY DIFFRACTIONf_angle_d0.8350929397984338
X-RAY DIFFRACTIONf_chiral_restr0.0481344704692482
X-RAY DIFFRACTIONf_plane_restr0.00560698238084564
X-RAY DIFFRACTIONf_dihedral_angle_d19.56854540681905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.70002-1.72930.2932839064071120.2547121270982439X-RAY DIFFRACTION99.222092571
1.7293-1.76080.2873649285551220.2297820727122470X-RAY DIFFRACTION99.9228989977
1.7608-1.79460.2433123387361420.2175034862062424X-RAY DIFFRACTION99.8443579767
1.7946-1.83130.239389216631610.2047591433232424X-RAY DIFFRACTION100
1.8313-1.87110.2196351541881330.1913740132782452X-RAY DIFFRACTION99.922690375
1.8711-1.91460.256083438905990.1875864402282499X-RAY DIFFRACTION99.9615236629
1.9146-1.96250.2166924303551490.1862675342312443X-RAY DIFFRACTION100
1.9625-2.01560.196725623081440.1767362004962461X-RAY DIFFRACTION100
2.0156-2.07490.1946250369771440.1735721845892456X-RAY DIFFRACTION100
2.0749-2.14180.1966648199471290.1693417157942477X-RAY DIFFRACTION100
2.1418-2.21840.2061265100681480.1648295744972478X-RAY DIFFRACTION100
2.2184-2.30720.2071108468021250.1691229909352495X-RAY DIFFRACTION99.9237223494
2.3072-2.41220.2110205348921310.1586723758282514X-RAY DIFFRACTION100
2.4122-2.53930.1739944988021330.155137428632482X-RAY DIFFRACTION100
2.5393-2.69840.2112436045761300.165002052692538X-RAY DIFFRACTION100
2.6984-2.90670.1804189547861540.1611114888162495X-RAY DIFFRACTION100
2.9067-3.19910.1707858109561470.169923791672542X-RAY DIFFRACTION100
3.1991-3.66180.1629072186551360.1640781035212574X-RAY DIFFRACTION100
3.6618-4.61250.1533488924411540.1446420976862605X-RAY DIFFRACTION99.9275624774
4.6125-41.52740.177492760911420.1801520116822825X-RAY DIFFRACTION99.8317631225
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)
11.477226300520.503913194661-0.4964328679721.378168631830.5593804910732.05278429131-0.0225370635710.0223255363045-0.0318786794244-0.07822189386570.0170886950259-0.081745368272-0.1723969199370.1418281147970.01961933403760.118586190619-0.0279616018438-0.007425379156060.08830004020770.008227388184690.1618438200463.9790655739412.62249533095.24399709738
21.03154073932-0.497934440699-1.035248477510.2633820296180.2160306582695.16105329352-0.0198114513559-0.02259102342030.370026672460.1520239055670.133507064535-0.0727256231752-0.921004070298-0.154684311654-0.02442474767070.4624122599250.100078135512-0.06068514742470.196701757191-0.0341462084870.297256231744-16.438221108734.046939075714.8209838883
30.605615161406-0.0889183749491-0.129629185330.63160832496-0.03564319831731.023791340480.00629127134957-0.005755444989360.01870835586180.0194364747612-0.04148287976760.0394261143826-0.358398977787-0.040376094250.04068228932860.2263370500770.00114719386618-0.02640646355130.072894756395-0.006205235114960.149879714043-8.9679357909722.800600962610.2084580534
40.4936566837820.1956463219820.04732947893440.931736883244-0.3481199609450.847792484725-0.066403265934-0.03183331604540.1181298985560.08783967359680.0203314569291-0.0338505146293-0.569544321230.00994328495002-0.006787157283730.291720933392-0.025761250014-0.03800688621160.0685345079406-0.00477067094050.151343188892-6.0523548202623.281526133620.6844691655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 328 )
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 396 )

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