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- PDB-9rjj: Structure of Mycobacterium tuberculosis InhA in complex with pyri... -

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Basic information

Entry
Database: PDB / ID: 9rjj
TitleStructure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV37a (compound 9)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA mycobacterium tuberculosis pyridomycin complex inhibitor
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis '98-R604 INH-RIF-EM' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å
AuthorsPublicola, G. / Mourey, L. / Valderrama, K. / Hartkoorn, R. / Maveyraud, L.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE44-0002 France
CitationJournal: J.Med.Chem. / Year: 2026
Title: Optimizing the Antibiotic Potency and Metabolic Stability of Pyridomycin Using a Semisynthetic Approach.
Authors: Valderrama, K. / Horlacher, O. / Publicola, G. / Eisenring, P. / Kienle, M. / Boarbi, S. / Kiass, M. / Kordulakova, J. / Chatagnon, J. / Piveteau, C. / Leroux, F. / Savkova, K. / Zahorszka, ...Authors: Valderrama, K. / Horlacher, O. / Publicola, G. / Eisenring, P. / Kienle, M. / Boarbi, S. / Kiass, M. / Kordulakova, J. / Chatagnon, J. / Piveteau, C. / Leroux, F. / Savkova, K. / Zahorszka, M. / Cantrelle, F.X. / Lherbet, C. / Mourey, L. / Mikusova, K. / Mathys, V. / Aichholz, R. / Maveyraud, L. / Altmann, K.H. / Hartkoorn, R.C.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 25, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,80011
Polymers173,0226
Non-polymers2,7785
Water15,565864
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5718
Polymers115,3484
Non-polymers2,2224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14200 Å2
ΔGint-99 kcal/mol
Surface area35470 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0157
Polymers115,3484
Non-polymers1,6673
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14080 Å2
ΔGint-102 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.92, 82.54, 187.99
Angle α, β, γ (deg.)90, 95.79, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / ENR / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28837.057 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis '98-R604 INH-RIF-EM' (bacteria)
Gene: inhA, Rv1484, MTCY277.05 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-A1JG0 / ~{N}-[(2~{Z},5~{R},6~{S},9~{S},10~{S},11~{R})-2-butan-2-ylidene-5,11-dimethyl-10-oxidanyl-3,7,12-tris(oxidanylidene)-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-6-yl]-2,3-bis(oxidanyl)benzamide


Mass: 555.576 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C28H33N3O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 30% PEG 550 MME 0.1 M NaCl 0.1 M Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.08→187.03 Å / Num. obs: 87988 / % possible obs: 96.3 % / Redundancy: 7.01 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.996 / CC1/2 anomalous: -0.021 / Rmerge(I) obs: 0.1707 / Rpim(I) all: 0.0691 / Rrim(I) all: 0.1844 / AbsDiff over sigma anomalous: 0.8 / Net I/σ(I): 8.92 / Num. measured all: 616955 / % possible anomalous: 95.8 / Redundancy anomalous: 3.58
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
5.647-187.036.780.051226.613199131991472047200.998-0.0960.02110.05550.75299.93.5699.8
4.482-5.6477.210.071822.963341033410463546350.997-0.0340.02860.07730.8121003.71100
3.915-4.4827.380.074422.893382933829458545850.997-0.0360.02930.080.8111003.78100
3.557-3.9156.650.094417.752254822548338933890.994-0.0040.03910.10230.84871.53.4873.8
3.302-3.5576.420.12114.422420124201376837680.991-0.0140.05160.13180.84680.53.3382.3
3.108-3.3027.020.157512.183193531935455245520.9880.0220.0640.17010.8799.83.57100
2.952-3.1087.140.20379.663250932509455345530.982-0.0140.08170.21960.851003.63100
2.823-2.9527.230.23828.593297532975455945590.976-0.0060.09480.25650.8251003.68100
2.715-2.8237.290.30666.823335433354457745770.964-0.010.12130.32990.8141003.7100
2.621-2.7157.280.37855.723330933309457745770.947-0.0170.150.40740.82299.93.69100
2.539-2.6217.220.41915.023296532965456445640.933-0.0260.16680.45140.7961003.67100
2.467-2.5396.810.48744.193088630886453645360.904-0.0380.20060.52770.8081003.47100
2.402-2.4676.550.50693.922968129681453145310.891-0.0230.21480.55150.7961003.33100
2.343-2.4026.850.5643.633133631336457445740.878-0.0030.2320.61050.7851003.48100
2.29-2.3437.010.64133.213196131961456045600.856-0.0090.25990.69250.7841003.55100
2.241-2.296.710.7832.582291622916341734170.757-0.0170.32450.84880.77373.93.4475.9
2.196-2.2416.780.86992.292935129351433043300.741-0.0230.3580.94230.75690.93.4993.9
2.155-2.1967.170.8662.373211232112448044800.764-0.0160.34550.93310.74499.93.63100
2.116-2.1557.241.031623315433154457845780.705-0.0020.40911.11060.7611003.66100
2.08-2.1167.221.22581.663253232532450345030.643-0.0120.48621.31970.75399.83.6599.9

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20230726data processing
XSCALEdata scaling
TRUNCATE9.0.004data processing
BUSTER2.10.4refinement
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.08→30.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.236 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4424 -RANDOM
Rwork0.1853 ---
obs0.1869 87955 96.2 %-
Displacement parametersBiso mean: 36.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.8408 Å20 Å21.6875 Å2
2---0.1975 Å20 Å2
3----2.6433 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.08→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11675 0 200 864 12739
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812233HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.916636HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4166SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2123HARMONIC5
X-RAY DIFFRACTIONt_it12233HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1634SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11692SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion15.79
LS refinement shellResolution: 2.08→2.09 Å
RfactorNum. reflection% reflection
Rfree0.2783 92 -
Rwork0.2584 --
obs0.2594 1760 97.48 %
Refinement TLS params.

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)
11.13530.13710.11020.7125-0.04160.73240.0007-0.09470.0694-0.0947-0.04340.19680.06940.19680.0427-0.06280.02520.022-0.0680.0366-0.07185.1769-33.603278.3481
21.09330.07740.11230.4502-0.0790.7276-0.0244-0.0694-0.0764-0.06940.0368-0.1973-0.0764-0.1973-0.0124-0.09530.0333-0.0304-0.07210.0264-0.0922-24.733-23.373678.3451
30.7972-0.26180.14211.3311-0.22331.61750.0931-0.34030.2303-0.3403-0.01940.21870.23030.2187-0.0737-0.05280.0766-0.033-0.1129-0.0372-0.2004-36.1194-31.635712.1885
40.8868-0.0676-0.03481.17770.05611.48060.06890.0570.43420.0570.02130.13410.43420.1341-0.0902-0.02140.0785-0.0824-0.1919-0.0003-0.1445-40.9784-47.177739.8248
50.9109-0.6509-0.02941.3141-0.04630.3345-0.02070.1060.10630.1060.0262-0.06140.1063-0.0614-0.00550.2338-0.1229-0.0975-0.01880.1220.1879-8.0884-62.77247.7416
60.9664-0.628-0.27990.59740.0616-0.0667-0.24270.0367-0.23480.03670.0963-0.0329-0.2348-0.03290.14640.0548-0.18590.11670.20250.11340.35112.2937-46.441428.725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 269
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B3 - 269
4X-RAY DIFFRACTION2{ B|* }B301
5X-RAY DIFFRACTION3{ C|* }C3 - 269
6X-RAY DIFFRACTION4{ D|* }D3 - 269
7X-RAY DIFFRACTION4{ D|* }D301
8X-RAY DIFFRACTION5{ E|* }E3 - 269
9X-RAY DIFFRACTION5{ E|* }E301
10X-RAY DIFFRACTION6{ F|* }F3 - 269
11X-RAY DIFFRACTION6{ F|* }F301

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