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- PDB-1p45: Targeting tuberculosis and malaria through inhibition of enoyl re... -

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Basic information

Entry
Database: PDB / ID: 1p45
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 / triclosan / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / 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: 2.6 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.N. / 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: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3057
Polymers57,1102
Non-polymers2,1955
Water81145
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)118,61014
Polymers114,2194
Non-polymers4,39110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area22940 Å2
ΔGint-245 kcal/mol
Surface area33900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.822, 104.120, 189.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: INHA OR RV1484 OR MT1531 OR 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.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6.8 / 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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 27704 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
% possible obs: 95.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / SU B: 12.02 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28969 1401 5.1 %RANDOM
Rwork0.22509 ---
obs0.2283 26302 94.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--5.74 Å20 Å2
3----5.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3987 0 139 45 4171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0214213
X-RAY DIFFRACTIONr_bond_other_d0.0110.023878
X-RAY DIFFRACTIONr_angle_refined_deg2.942.0015738
X-RAY DIFFRACTIONr_angle_other_deg1.34138974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.345534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.160.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024682
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02826
X-RAY DIFFRACTIONr_nbd_refined0.2650.21163
X-RAY DIFFRACTIONr_nbd_other0.2640.24703
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.110.22446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.081.52649
X-RAY DIFFRACTIONr_mcangle_it1.96824217
X-RAY DIFFRACTIONr_scbond_it3.12231564
X-RAY DIFFRACTIONr_scangle_it4.9784.51521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 68
Rwork0.413 1454
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Num. reflection obs: 27704 / % reflection Rfree: 10 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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