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- PDB-5oif: InhA (T2A mutant) complexed with 1-benzyl-3-methyl-1H-pyrazol-5-amine -

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Basic information

Entry
Database: PDB / ID: 5oif
TitleInhA (T2A mutant) complexed with 1-benzyl-3-methyl-1H-pyrazol-5-amine
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Inhibitor / complex / fragment based drug discovery / tuberculosis
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-methyl-2-(phenylmethyl)pyrazol-3-amine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsConvery, M.A.
CitationJournal: ChemMedChem / Year: 2018
Title: Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.
Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / ...Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / Green, S.R. / Huggett, M. / Barros, D. / Wyatt, P.G. / Ray, P.C.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7516
Polymers57,0502
Non-polymers1,7014
Water5,747319
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)117,50212
Polymers114,0994
Non-polymers3,4038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_957-x+4,y,-z+21
MethodPISA
Unit cell
Length a, b, c (Å)73.390, 113.860, 65.750
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28524.754 Da / Num. of mol.: 2 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-9W5 / 5-methyl-2-(phenylmethyl)pyrazol-3-amine


Mass: 187.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.17% MPD, 0.3M Mg(NO3)2, 0.1M Tris pH8 and 20% PEG2K Cryo - well soln

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.03→56.93 Å / Num. obs: 32020 / % possible obs: 95.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.036 / Net I/σ(I): 7.2
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.812 / Num. unique obs: 2444 / CC1/2: 0.531 / Χ2: 1.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementResolution: 2.03→26.58 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9013 / SU R Cruickshank DPI: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1579 4.93 %RANDOM
Rwork0.1744 ---
obs0.1767 32008 94.95 %-
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.3804 Å20 Å2-4.2197 Å2
2---5.0428 Å20 Å2
3---5.4232 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: 1 / Resolution: 2.03→26.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 116 319 4331
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014100HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075585HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1401SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it4100HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion17.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion546SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4988SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.1 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2388 158 5.2 %
Rwork0.2135 2881 -
all0.2148 3039 -
obs--94.95 %
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)
10.54660.08210.10330.3594-0.21891.19720.0767-0.0762-0.08420.0547-0.0782-0.00530.00580.07610.00150.0234-0.0459-0.024-0.09260.0215-0.0469131.7647-14.652279.7472
20.6045-0.00690.13170.60190.04660.68910.0907-0.060.10.0587-0.0923-0.0539-0.17450.0510.00160.039-0.08110.0026-0.0864-0.0093-0.049139.939616.567276.0062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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