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- PDB-6sql: Crystal structure of M. tuberculosis InhA in complex with NAD+ an... -

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Basic information

Entry
Database: PDB / ID: 6sql
TitleCrystal structure of M. tuberculosis InhA in complex with NAD+ and N-(3-(aminomethyl)phenyl)-5-chloro-3-methylbenzo[b]thiophene-2-sulfonamide
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / NADH-dependent enoyl-[acyl-carrier-protein] reductase
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 / 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-LTK / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsMendes, V. / Sabbah, M. / Coyne, A.G. / Abell, C. / Blundell, T.L.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme260872 United Kingdom
Bill & Melinda Gates FoundationOPP1158806 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment-Based Design ofMycobacterium tuberculosisInhA Inhibitors.
Authors: Sabbah, M. / Mendes, V. / Vistal, R.G. / Dias, D.M.G. / Zahorszka, M. / Mikusova, K. / Kordulakova, J. / Coyne, A.G. / Blundell, T.L. / Abell, C.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,6723
Polymers28,6421
Non-polymers1,0302
Water2,720151
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)118,68912
Polymers114,5674
Non-polymers4,1218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area18880 Å2
ΔGint-128 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.931, 97.931, 139.954
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

21A-464-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28641.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, 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-LTK / ~{N}-[3-(aminomethyl)phenyl]-5-chloranyl-3-methyl-1-benzothiophene-2-sulfonamide


Mass: 366.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15ClN2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0 0.1 M sodium acetate 25-30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.35→84.8 Å / Num. obs: 17416 / % possible obs: 99 % / Redundancy: 18.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.085 / Rrim(I) all: 0.369 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.4819.62.1264764424370.90.492.1833.899.9
7.44-84.8150.11197916540.9960.0290.11525.3100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.93 Å84.81 Å
Translation6.93 Å84.81 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.15data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B35

2b35


Resolution: 2.35→84.8 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.39
RfactorNum. reflection% reflection
Rfree0.204 861 4.94 %
Rwork0.1621 --
obs0.1642 17416 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.21 Å2 / Biso mean: 32.4674 Å2 / Biso min: 12.12 Å2
Refinement stepCycle: final / Resolution: 2.35→84.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 67 151 2206
Biso mean--41.61 39.86 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.35-2.48330.28071150.20192686
2.4833-2.6750.23561400.1922703
2.675-2.94420.25291420.18832713
2.9442-3.37030.2181550.16582719
3.3703-4.24620.17891450.13792789
4.2462-84.80.17721640.15182945
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)
12.1943-0.2277-0.29310.92320.33711.01180.07780.14180.3426-0.04440.0049-0.1994-0.41290.085-0.14620.4305-0.1218-0.02210.17560.0460.3026-35.095527.142-5.6858
22.1998-0.9720.93782.9875-1.36421.9893-0.0370.3410.3453-0.2751-0.0801-0.0903-0.12890.69290.14340.4979-0.2326-0.01520.31280.05690.3188-24.12827.2316-8.825
31.2744-0.03850.62710.88470.44921.45010.07690.00590.13970.3517-0.0796-0.3635-0.28930.53510.04040.4071-0.2572-0.03630.45260.08220.3529-21.531324.05131.5226
41.30520.42660.41750.95770.11970.5298-0.03-0.27810.10360.2044-0.1251-0.2094-0.4070.5255-0.00280.3592-0.1549-0.03280.29170.01690.2435-29.346819.97541.2225
50.947-0.0954-0.06871.1732-0.15050.6326-0.01270.08810.0293-0.0054-0.0603-0.0954-0.10360.27840.0560.1716-0.0484-0.0180.24040.04880.2028-31.7096.9143-1.4103
61.0346-0.4059-0.09980.9621-0.27881.25970.00810.17340.0317-0.3016-0.0095-0.0743-0.22080.10470.02120.2545-0.04460.00390.13310.01170.2207-42.485512.9257-11.3069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )A3 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 53 )A33 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 82 )A54 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 99 )A83 - 99
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 182 )A100 - 182
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 269 )A183 - 269

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