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- PDB-5g0s: InhA in complex with a DNA encoded library hit -

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Basic information

Entry
Database: PDB / ID: 5g0s
TitleInhA in complex with a DNA encoded library hit
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / INHA / ACP ENOYL REDUCTASE / DNA ENCODED LIBRARY / DEL / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EEH / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRead, J.A. / Breed, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Discovery of Cofactor-Specific, Bactericidal Mycobacterium Tuberculosis Inha Inhibitors Using DNA-Encoded Library Technology
Authors: Soutter, H.H. / Centrella, P. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Guie, M.-A. / Habeshian, S. / Keefe, A.D. / Kennedy, K.M. / Sigel, E.A. / Troast, D.M. / Zhang, Y. / Ferguson, A. ...Authors: Soutter, H.H. / Centrella, P. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Guie, M.-A. / Habeshian, S. / Keefe, A.D. / Kennedy, K.M. / Sigel, E.A. / Troast, D.M. / Zhang, Y. / Ferguson, A.D. / Davies, G. / Stead, E.R. / Breed, J. / Madhavapeddi, P. / Read, J.A.
History
DepositionMar 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,05010
Polymers114,2194
Non-polymers3,8316
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21030 Å2
ΔGint-141.6 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.322, 112.654, 68.121
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / NADH-DEPENDENT ENOYL-ACP REDUCTASE / ENOYL-ACYL CARRIER PROTEIN REDUCTASE


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-EEH / N-[4-[2-[(2S)-4-[2-(methylamino)-2-oxidanylidene-ethyl]-3-oxidanylidene-2-(phenylmethyl)piperazin-1-yl]-2-oxidanylidene-ethyl]cyclohexyl]-2-(3-methyl-1-benzothiophen-2-yl)ethanamide


Mass: 588.760 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.17 Å3/Da / Density % sol: 43.36 % / Description: NONE
Crystal growpH: 7.2 / Details: pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 21, 2014 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.74→57.9 Å / Num. obs: 97477 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 25.04 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 1.74→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOSFLMdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0R

4d0r


Resolution: 1.74→57.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9483 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 4803 4.93 %RANDOM
Rwork0.1625 ---
obs0.1636 97445 97.68 %-
Displacement parametersBiso mean: 29.12 Å2
Baniso -1Baniso -2Baniso -3
1-5.1586 Å20 Å2-1.9054 Å2
2---1.7933 Å20 Å2
3----3.3653 Å2
Refine analyzeLuzzati coordinate error obs: 0.198 Å
Refinement stepCycle: LAST / Resolution: 1.74→57.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7605 0 260 910 8775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018058HARMONIC2
X-RAY DIFFRACTIONt_angle_deg111005HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2683SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1285HARMONIC5
X-RAY DIFFRACTIONt_it8058HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion14.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1098SEMIHARMONIC5
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_contact10021SEMIHARMONIC4
LS refinement shellResolution: 1.74→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2386 310 4.83 %
Rwork0.2174 6106 -
all0.2185 6416 -
obs--97.68 %
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)
10.9218-0.18620.00920.67820.07150.5711-0.0148-0.02430.09930.08070.0006-0.0054-0.1251-0.12940.0141-0.01820.0140.0197-0.0083-0.0115-0.05320.277213.862428.7179
20.7689-0.19130.09330.75640.10850.56470.00860.0692-0.2145-0.0323-0.0274-0.14430.16490.01630.0188-0.0452-0.00450.0391-0.0763-0.03930.071623.2256-19.053512.8015
30.7394-0.2538-0.12720.62380.16070.86250.02710.3039-0.0886-0.1601-0.071-0.007-0.0189-0.1690.0439-0.032200.02790.0754-0.0306-0.08534.9972.2473-1.4282
40.5214-0.04850.07560.54620.07340.52060.006-0.0457-0.01570.12660.01-0.2479-0.03750.0813-0.016-0.0503-0.0235-0.0429-0.0393-0.00780.059429.16723.475635.0047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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