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- PDB-5g0w: InhA in complex with a DNA encoded library hit -

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Basic information

Entry
Database: PDB / ID: 5g0w
TitleInhA in complex with a DNA encoded library hit
ComponentsENOYL-ACYL CARRIER PROTEIN REDUCTASE
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 / fatty acid biosynthetic process / 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-9NU / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: ENOYL-ACYL CARRIER PROTEIN REDUCTASE
C: ENOYL-ACYL CARRIER PROTEIN REDUCTASE
D: ENOYL-ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,12313
Polymers114,2194
Non-polymers3,9049
Water17,511972
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21790 Å2
ΔGint-167.2 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.428, 112.729, 67.970
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
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: M9TGV3, UniProt: P9WGR1*PLUS, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-9NU / (2S,4S)-N-methyl-4-[[(2S,3R)-3-[(2-methylpropan-2-yl)oxy]-2-[[4-(pyrazol-1-ylmethyl)phenyl]carbonylamino]butanoyl]amino]-1-(phenylcarbonyl)pyrrolidine-2-carboxamide


Mass: 588.697 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H40N6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 43.45 % / 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: 1.79→57.8 Å / Num. obs: 90585 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 24.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 1.79→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1

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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: 1.79→57.83 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 4454 4.93 %RANDOM
Rwork0.1646 ---
obs0.166 90354 98.45 %-
Displacement parametersBiso mean: 28.21 Å2
Baniso -1Baniso -2Baniso -3
1-5.3216 Å20 Å2-2.0889 Å2
2---4.114 Å20 Å2
3----1.2076 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.79→57.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7611 0 265 972 8848
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018082HARMONIC2
X-RAY DIFFRACTIONt_angle_deg111046HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2692SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1302HARMONIC5
X-RAY DIFFRACTIONt_it8082HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion16.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1109SEMIHARMONIC5
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_contact10084SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2458 376 5.65 %
Rwork0.2245 6284 -
all0.2257 6660 -
obs--98.45 %
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)
11.025-0.28120.08590.590.08970.8353-0.02020.00250.08640.0765-0.0067-0.0041-0.1394-0.19380.0269-0.02180.03110.01310.0209-0.0124-0.0810.143913.703429.096
20.6669-0.28520.04420.70120.12060.6903-0.00890.0746-0.16-0.0274-0.0189-0.0940.1699-0.00870.0277-0.0204-0.00250.0403-0.0452-0.030.002923.8162-19.068812.8971
31.1982-0.4747-0.12470.63980.11720.7010.08760.399-0.0796-0.1732-0.11480.0004-0.0351-0.18260.0272-0.03360.02280.01520.1279-0.0286-0.12755.07661.9457-1.0801
40.6614-0.01270.13320.59250.07090.6784-0.0005-0.0187-0.00040.10330.0321-0.2099-0.02880.1092-0.0316-0.0497-0.013-0.0339-0.0187-0.0090.007529.52263.54535.1872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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