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- PDB-4d0r: Mtb InhA complex with Pyradizinone compound 1 -

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Basic information

Entry
Database: PDB / ID: 4d0r
TitleMtb InhA complex with Pyradizinone compound 1
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / ACP ENOYL REDUCTASE / METHYL-THIAZOLE
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-41I / 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: 2.75 Å
AuthorsRead, J.A. / Gingell, H. / Madhavapeddi, P. / Lange, S.
CitationJournal: To be Published
Title: Pyridazinones: A Novel Scaffold with Excellent Physicochemical Properties and Safety Profile for a Clinically Validated Target of Mycobacterium Tuberculosis
Authors: Lange, S.
History
DepositionApr 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5613
Polymers28,5561
Non-polymers1,0052
Water32418
1
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,24412
Polymers114,2234
Non-polymers4,0218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area22390 Å2
ΔGint-140.4 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.997, 96.997, 139.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / NADH-DEPENDENT ENOYL-ACP REDUCTASE / ENOYL-ACYL CARRIER PROTEIN REDUCTASE


Mass: 28555.766 Da / Num. of mol.: 1
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 / Variant (production host): STAR
References: UniProt: P9WGR0, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-41I / 4-(4-chlorophenoxy)-6-oxo-1-phenyl-1,6-dihydropyridazine-3-carboxamide


Mass: 341.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12ClN3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.31 Å3/Da / Density % sol: 62.82 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Feb 7, 2013 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→84 Å / Num. obs: 10586 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2.75→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 92

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→84 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.9168 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.6 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 506 4.82 %RANDOM
Rwork0.2167 ---
obs0.2179 10491 98.82 %-
Displacement parametersBiso mean: 54.95 Å2
Baniso -1Baniso -2Baniso -3
1--4.3758 Å20 Å20 Å2
2---4.3758 Å20 Å2
3---8.7517 Å2
Refinement stepCycle: LAST / Resolution: 2.75→84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 68 18 2010
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082035HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062780HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d662SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2035HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion19.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
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_contact2418SEMIHARMONIC4
LS refinement shellResolution: 2.75→3.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3172 138 4.73 %
Rwork0.2437 2780 -
all0.247 2918 -
obs--98.82 %
Refinement TLS params.Method: refined / Origin x: 51.6739 Å / Origin y: 47.3038 Å / Origin z: 18.5353 Å
111213212223313233
T-0.1779 Å2-0.014 Å2-0.0081 Å2-0.0974 Å2-0.0278 Å2---0.1157 Å2
L1.2194 °2-0.0887 °20.3855 °2-0.6723 °20.2274 °2--1.1415 °2
S-0.014 Å °0.0674 Å °0.0553 Å °-0.0026 Å °-0.0695 Å °0.2005 Å °-0.1458 Å °-0.495 Å °0.0835 Å °
Refinement TLS groupSelection details: CHAIN A

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