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- PDB-3fnf: Crystal structure of InhA bound to triclosan derivative -

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Basic information

Entry
Database: PDB / ID: 3fnf
TitleCrystal structure of InhA bound to triclosan derivative
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / triclosan / tuberculosis / Antibiotic resistance / Fatty acid biosynthesis / Lipid synthesis / NAD
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 ...enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 / 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-benzyl-2-(2,4-dichlorophenoxy)phenol / 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: 2.3 Å
AuthorsWang, F.
CitationJournal: Chemmedchem / Year: 2009
Title: Triclosan Derivatives: Towards Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis.
Authors: Freundlich, J.S. / Wang, F. / Vilcheze, C. / Gulten, G. / Langley, R. / Schiehser, G.A. / Jacobus, D.P. / Jacobs, W.R. / Sacchettini, J.C.
History
DepositionDec 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)118,25412
Polymers114,2194
Non-polymers4,0358
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-124 kcal/mol
Surface area33440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.651, 92.377, 102.406
Angle α, β, γ (deg.)90.00, 106.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-308-

HOH

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Components

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


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MT1531, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, 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-JPM / 5-benzyl-2-(2,4-dichlorophenoxy)phenol


Mass: 345.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H14Cl2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 3350, 6% DMSO, 0.1M ADA pH 6.8, and 0.08 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 121 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48113 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.087 / Rsym value: 0.103 / Net I/σ(I): 28.6
Reflection shellResolution: 2.3→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3799 / Rsym value: 0.883 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ENY

1eny


Resolution: 2.3→19.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.95 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2508 5.1 %RANDOM
Rwork0.2 ---
obs0.20305 46976 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.01 Å2
2--0.11 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7739 0 268 253 8260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7092.00611139
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93751028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46723.766308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.245151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6041552
X-RAY DIFFRACTIONr_chiral_restr0.1240.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026120
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.24458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25482
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7081.55249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1828167
X-RAY DIFFRACTIONr_scbond_it1.92833365
X-RAY DIFFRACTIONr_scangle_it2.8864.52972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 166 -
Rwork0.264 2955 -
obs--86 %

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