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- PDB-6te7: The structure of CYP121 in complex with inhibitor S2 -

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Basic information

Entry
Database: PDB / ID: 6te7
TitleThe structure of CYP121 in complex with inhibitor S2
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / CYP121 / complex / inhibitor
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-N55 / TRIETHYLENE GLYCOL / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50001818022 Å
AuthorsAdam, S. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKO 4116/3-1 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 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
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)44,4455
Polymers43,3061
Non-polymers1,1404
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.487, 77.487, 263.746
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-1366-

HOH

21A-1377-

HOH

31A-1442-

HOH

41A-1508-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 514 molecules

#2: Chemical ChemComp-N55 / 2-chloranyl-4-[4-[(1~{R})-1-imidazol-1-ylprop-2-enyl]phenyl]phenol


Mass: 310.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15ClN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
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: X10SA / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→47.03 Å / Num. obs: 75979 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 15.0043979259 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.047 / Net I/σ(I): 9.2
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.686 / Num. unique obs: 10867 / CC1/2: 0.746 / Rrim(I) all: 0.339

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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: 1.50001818022→41.4706717953 Å / SU ML: 0.133294973417 / Cross valid method: FREE R-VALUE / σ(F): 1.33590715916 / Phase error: 17.5294066846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.184044131729 3801 5.01028155647 %
Rwork0.164570437032 72063 -
obs0.165558768708 75864 99.7593593436 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.7222416225 Å2
Refinement stepCycle: LAST / Resolution: 1.50001818022→41.4706717953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 36 510 3601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01105667410843215
X-RAY DIFFRACTIONf_angle_d1.193226591044397
X-RAY DIFFRACTIONf_chiral_restr0.0617931935345484
X-RAY DIFFRACTIONf_plane_restr0.00908713832277568
X-RAY DIFFRACTIONf_dihedral_angle_d18.05800869041917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.50002-1.5190.2634648079421260.2501180236672660X-RAY DIFFRACTION99.6067214873
1.519-1.5390.2841951444491170.2468292961542582X-RAY DIFFRACTION99.5573589082
1.539-1.56010.2265833042521430.2289313929322622X-RAY DIFFRACTION99.5678790061
1.5601-1.58240.2465174205131530.2238580453612600X-RAY DIFFRACTION99.5660036166
1.5824-1.6060.2427557269421470.2174687185972593X-RAY DIFFRACTION99.6726082212
1.606-1.63110.212819687791340.216087924462611X-RAY DIFFRACTION99.4204998189
1.6311-1.65780.2258945985011350.2085881035072624X-RAY DIFFRACTION99.8552298227
1.6578-1.68640.2178137163941380.2003549763992644X-RAY DIFFRACTION99.7490139835
1.6864-1.71710.2667109897331530.1932407718882587X-RAY DIFFRACTION99.3833877403
1.7171-1.75010.210747274821310.194528103132639X-RAY DIFFRACTION99.8558038933
1.7501-1.78580.2195854282611240.1821662171322651X-RAY DIFFRACTION99.8201438849
1.7858-1.82470.2068937082031390.1817862862312621X-RAY DIFFRACTION99.9275887038
1.8247-1.86710.2065061778581390.1825696539872657X-RAY DIFFRACTION99.7858672377
1.8671-1.91380.2074122823231180.1710791566992662X-RAY DIFFRACTION99.9640417116
1.9138-1.96550.1640927146551430.1652491820722644X-RAY DIFFRACTION99.8924731183
1.9655-2.02340.1779360323341400.1628371854322661X-RAY DIFFRACTION100
2.0234-2.08870.1633786670441210.1615887802162671X-RAY DIFFRACTION99.7142857143
2.0887-2.16330.1802640940281620.1540922780372642X-RAY DIFFRACTION99.8575498575
2.1633-2.24990.1854712399791340.1467996542632658X-RAY DIFFRACTION99.8212370397
2.2499-2.35230.1643404903681490.1399846484472694X-RAY DIFFRACTION100
2.3523-2.47630.1676741135721640.1415277237372657X-RAY DIFFRACTION99.9645641389
2.4763-2.63150.1533261698061450.1462635801662699X-RAY DIFFRACTION99.9297259311
2.6315-2.83460.1861948962041350.146129156812708X-RAY DIFFRACTION99.8244382022
2.8346-3.11980.1862662524611620.1616332720292702X-RAY DIFFRACTION99.5481404241
3.1198-3.5710.1729093418291400.1503138199622763X-RAY DIFFRACTION99.8280605227
3.571-4.49820.1651630064641520.1372074450152804X-RAY DIFFRACTION99.8986143968
4.4982-41.4690.1708529097721570.1798315458553007X-RAY DIFFRACTION99.4968553459
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)
10.9937097075130.380987981097-0.04880027420590.6682714914390.2096420413131.30648871409-0.00581303119553-0.032144954280.0391831162983-0.03053445292760.0162556897367-0.0473463612445-0.1390787957860.0784869873016-0.002987998440910.0962274885062-0.01065910004340.005174734001080.07319486565340.002065563596860.1184442861083.7724969008112.63940206345.21282072135
20.627346882456-0.2115777246930.2064831625450.438537834454-0.2546691779921.33793624159-0.053873328313-0.01901490146960.1441379248170.02650142140610.0211442455293-0.0147199143021-0.426835716418-0.1433675153160.02359098045280.1864136937090.0306354839627-0.008494451868610.0895941930501-0.0002591953104850.135482588319-17.806065891525.987538580314.4327020086
30.723418717985-0.1434197090630.316742838330.922459839501-0.7558792264711.07292657204-0.02341219628140.08345623127180.0733443549022-0.136679235178-0.01919333151980.102080869589-0.182277756493-0.06970463926120.05182492339090.1668078381990.0384190338438-0.0124011448810.0946707807319-0.009932893347560.120154209185-18.729889852724.8287434151.94113951324
40.717579136175-0.00514081519572-0.5179215512820.288310228073-0.2148075577911.296892660950.0646861222007-0.06565752792250.09198974975720.041058605689-0.0251065531019-0.0549596956627-0.3756289124610.139705347674-0.03918424131490.182255015092-0.0529795000339-0.01061950035120.0775840125903-0.003505508379780.114283106562-0.080936334659122.973758933718.0061501023
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 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 250 )
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 396 )

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