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- PDB-1p44: Targeting tuberculosis and malaria through inhibition of enoyl re... -

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Basic information

Entry
Database: PDB / ID: 1p44
TitleTargeting tuberculosis and malaria through inhibition of enoyl reductase: compound activity and structural data
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / short chain dehydrogenase reductase / inhibitor / rossmann fold / enoyl-ACP reductase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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
Chem-GEQ / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. ...Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. / Musser, J.M. / Kreiswirth, B. / Iwamoto, H. / Perozzo, R. / Jacobs Jr, W.R. / Sacchettini, J.C. / Fidock, D.A. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Targeting tuberculosis and malaria through inhibition of Enoyl reductase: compound activity and structural data.
Authors: Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. / Musser, J.M. / Kreiswirth, B. / Iwamoto, ...Authors: Kuo, M.R. / Morbidoni, H.R. / Alland, D. / Sneddon, S.F. / Gourlie, B.B. / Staveski, M.M. / Leonard, M. / Gregory, J.S. / Janjigian, A.D. / Yee, C. / Musser, J.M. / Kreiswirth, B. / Iwamoto, H. / Perozzo, R. / Jacobs, W.R. / Sacchettini, J.C. / Fidock, D.A.
History
DepositionApr 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,88316
Polymers171,3296
Non-polymers5,55410
Water2,648147
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)118,44712
Polymers114,2194
Non-polymers4,2288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,66010
Polymers114,2194
Non-polymers3,4416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20680 Å2
ΔGint-148 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.619, 83.219, 192.972
Angle α, β, γ (deg.)90.00, 94.95, 90.00
Int Tables number5
Space group name H-MC121

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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.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: INHA OR RV1484 OR MT1531 OR MTCY277.05 OR MB1520 / 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.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GEQ / 5-{[4-(9H-FLUOREN-9-YL)PIPERAZIN-1-YL]CARBONYL}-1H-INDOLE / GENZ-10850


Mass: 393.480 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H23N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM ADA, 150 mM ammonium acetate, 12% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
212 %PEG33501reservoir
3150 mMammonium acetate1reservoir
4100 mM[(carbamoylmethyl)imino]diacetic acid1reservoirpH6.8

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 38313 / % possible obs: 85.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 %
Reflection
*PLUS
Rmerge(I) obs: 0.085

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / σ(F): 0
RfactorNum. reflection
Rfree0.288 3833
Rwork0.19 -
obs-38313
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11964 0 384 147 12495
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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