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- PDB-5g0t: InhA in complex with a DNA encoded library hit -

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Basic information

Entry
Database: PDB / ID: 5g0t
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-S72 / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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)119,01112
Polymers114,2194
Non-polymers4,7928
Water19,3121072
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22870 Å2
ΔGint-131.2 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.166, 112.069, 67.847
Angle α, β, γ (deg.)90.00, 98.43, 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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-S72 / 1-benzyl-N-[cis-4-(2-{[(4-fluorophenyl)methyl][2-(methylamino)-2-oxoethyl]amino}-2-oxoethyl)cyclohexyl]-5-methyl-1H-1,2,3-triazole-4-carboxamide


Mass: 534.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H35FN6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1072 / 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: 2.15 Å3/Da / Density % sol: 42.67 % / 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.54→67.1 Å / Num. obs: 128781 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 1.54→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 89.8

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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: 1.54→67.11 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.9593 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.1818 6260 4.89 %RANDOM
Rwork0.1599 ---
obs0.161 127971 90.13 %-
Displacement parametersBiso mean: 21.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.1682 Å20 Å20.0253 Å2
2---1.3865 Å20 Å2
3----0.7817 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.54→67.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 332 1072 8853
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017983HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9810899HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2658SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1267HARMONIC5
X-RAY DIFFRACTIONt_it7983HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion13.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1075SEMIHARMONIC5
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_contact10097SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2387 454 4.85 %
Rwork0.2048 8905 -
all0.2065 9359 -
obs--90.13 %
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)
10.5566-0.08450.08540.42440.03070.4227-0.0064-0.03530.0720.0726-0.0180.0125-0.0946-0.08480.0245-0.0110.0150.01030.0092-0.0055-0.03830.233113.90728.6628
20.4008-0.17180.02150.57210.03760.4360.02250.0255-0.0951-0.0113-0.0178-0.09450.10970.0111-0.0047-0.01470.00250.0077-0.027800.019723.1445-19.113712.6903
30.3839-0.12120.0910.45450.04930.44920.01890.0993-0.0206-0.1029-0.0271-0.0116-0.0262-0.04390.0082-0.01080.00970.00950.03420.0045-0.05065.03062.5173-1.4918
40.32230.00040.03440.34470.03720.47790.0138-0.0325-0.01720.0978-0.0088-0.1398-0.01090.0485-0.005-0.024-0.0128-0.0383-0.00660.01030.020529.09453.378635.017
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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