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- PDB-4bqp: Mtb InhA complex with Methyl-thiazole compound 7 -

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Basic information

Entry
Database: PDB / ID: 4bqp
TitleMtb InhA complex with Methyl-thiazole compound 7
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / ACP ENOYL REDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 activity (NAD(P)H) / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-VMY / 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: 1.89 Å
AuthorsRead, J.A. / Gingell, H. / Madhavapeddi, P. / Shirude, P.S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Methyl-Thiazoles: A Novel Mode of Inhibition with the Potential to Develop Novel Inhibitors Targeting Inha in Mycobacterium Tuberculosis.
Authors: Shirude, P.S. / Madhavapeddi, P. / Naik, M. / Murugan, K. / Shinde, V. / Nandishaiah, R. / Bhat, J. / Kumar, A. / Hameed, S. / Holdgate, G. / Davies, G. / Mcmiken, H. / Hegde, N. / Ambady, A. ...Authors: Shirude, P.S. / Madhavapeddi, P. / Naik, M. / Murugan, K. / Shinde, V. / Nandishaiah, R. / Bhat, J. / Kumar, A. / Hameed, S. / Holdgate, G. / Davies, G. / Mcmiken, H. / Hegde, N. / Ambady, A. / Venkatraman, J. / Panda, M. / Bandodkar, B. / Sambandamurthy, V.K. / Read, J.A.
History
DepositionMay 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)177,93919
Polymers171,3296
Non-polymers6,61013
Water8,107450
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)118,65714
Polymers114,2194
Non-polymers4,43810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area19670 Å2
ΔGint-147.8 kcal/mol
Surface area32890 Å2
MethodPISA
2
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)118,61112
Polymers114,2194
Non-polymers4,3928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area19040 Å2
ΔGint-123.7 kcal/mol
Surface area31400 Å2
MethodPISA
3
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)118,61112
Polymers114,2194
Non-polymers4,3928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area19040 Å2
ΔGint-123.7 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.297, 81.304, 189.004
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2044-

HOH

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Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / ENOYL-ACYL CARRIER PROTEIN REDUCTASE / 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) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P0A5Y6, 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.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-VMY / (1S)-1-(5-{[1-(2,6-DIFLUOROBENZYL)-1H-PYRAZOL-3-YL]AMINO}-1,3,4-THIADIAZOL-2-YL)-1-(4-METHYL-1,3-THIAZOL-2-YL)ETHANOL


Mass: 434.486 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H16F2N6OS2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.26 Å3/Da / Density % sol: 45.62 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD / Date: May 12, 2012 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.89→60 Å / Num. obs: 113532 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 15.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.4
Reflection shellResolution: 1.89→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8.4 / % possible all: 79.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→19.05 Å / Cor.coef. Fo:Fc: 0.8592 / Cor.coef. Fo:Fc free: 0.8246 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.15
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=12287. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=12287. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 5629 5.02 %RANDOM
Rwork0.208 ---
obs0.2093 112158 91.78 %-
Displacement parametersBiso mean: 19.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.6993 Å20 Å2-1.3546 Å2
2--0.6895 Å20 Å2
3----4.3888 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 1.89→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11370 0 439 450 12259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112102HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0816560HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3936SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes219HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1930HARMONIC5
X-RAY DIFFRACTIONt_it12102HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion18.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1657SEMIHARMONIC5
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_contact14429SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 331 5.51 %
Rwork0.1996 5677 -
all0.2007 6008 -
obs--91.78 %
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)
11.1958-0.02110.1310.36150.25360.54470.02750.2483-0.0802-0.0812-0.0246-0.05430.02920.0588-0.0029-0.12320.0511-0.0069-0.0637-0.0143-0.122857.03057.596278.7558
21.0946-0.0111-0.36250.2074-0.2460.65610.01650.24170.0768-0.1142-0.00040.0198-0.0543-0.0597-0.0161-0.140.0673-0.0462-0.09940.0206-0.116926.84417.334678.6166
30.0995-0.120.0670.2215-0.17190.54960.00970.04750.0221-0.0306-0.024-0.0150.02010.02160.01430.05390.0602-0.00770.0029-0.0148-0.075214.22188.019211.9901
40.1998-0.1774-0.14330.51490.12750.0872-0.0024-0.0383-0.05360.00850.01250.02470.0209-0.0109-0.010.01990.0385-0.02720.00470.0073-0.048810.0026-6.769640.4891
50.19950.0578-0.09070.7096-0.24040.3825-0.0144-0.05610.0230.02880.01750.030.0073-0.0099-0.00310.01590.0973-0.03280.0314-0.0418-0.076443.8811-22.293248.2868
60.0529-0.1558-0.29440.74170.33970.1447-0.0035-0.00520.0809-0.019-0.0056-0.0316-0.02420.02770.0090.0240.0409-0.0239-0.0659-0.00510.023662.6427-5.761327.7069
70.0069-0.0302-0.02530.0001-0.001-0.00070.00050.0097-0.0038-0.01920.0187-0.00070.0041-0.0029-0.01920.00760.0202-0.0104-0.0042-0.0041-0.017635.8944-0.38148.1044
80.00430.0397-0.00660.04980.0264-0.00120.00470.02650.0064-0.004-0.0021-0.0021-0.0069-0.0052-0.00250.00340.0084-0.0031-0.0121-0.00920.001935.9137-0.364450.2092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F AND RESID 1271 OR CHAIN A AND RESID 1272
8X-RAY DIFFRACTION8CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F AND RESID 1270

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