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- PDB-6chq: Phosphopantetheine adenylyltransferase (CoaD) in complex with 2-b... -

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Basic information

Entry
Database: PDB / ID: 6chq
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with 2-benzyl-N-(3-chloro-4-methylphenyl)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / PPAT CaaD / FBDD Gram-negative antibacterial antibiotic / Transferase Transferase-antibiotic complex / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F0V / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 Å
AuthorsMamo, M. / Appleton, B.A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery and Optimization of Phosphopantetheine Adenylyltransferase Inhibitors with Gram-Negative Antibacterial Activity.
Authors: Skepper, C.K. / Moreau, R.J. / Appleton, B.A. / Benton, B.M. / Drumm, J.E. / Feng, B.Y. / Geng, M. / Hu, C. / Li, C. / Lingel, A. / Lu, Y. / Mamo, M. / Mergo, W. / Mostafavi, M. / Rath, C.M. ...Authors: Skepper, C.K. / Moreau, R.J. / Appleton, B.A. / Benton, B.M. / Drumm, J.E. / Feng, B.Y. / Geng, M. / Hu, C. / Li, C. / Lingel, A. / Lu, Y. / Mamo, M. / Mergo, W. / Mostafavi, M. / Rath, C.M. / Steffek, M. / Takeoka, K.T. / Uehara, K. / Wang, L. / Wei, J.R. / Xie, L. / Xu, W. / Zhang, Q. / de Vicente, J.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,53812
Polymers36,1482
Non-polymers1,39010
Water4,828268
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,61336
Polymers108,4436
Non-polymers4,17030
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
Buried area23880 Å2
ΔGint-348 kcal/mol
Surface area33430 Å2
MethodPISA
2
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)450,451144
Polymers433,77224
Non-polymers16,679120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_566-z,x+1,-y+11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_465y-1,-z+1,-x1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_444x-1/2,y-1/2,z-1/21
crystal symmetry operation14_574-x+1/2,-y+5/2,z-1/21
crystal symmetry operation15_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation16_475x-1/2,-y+5/2,-z+1/21
crystal symmetry operation17_453z-1/2,x+1/2,y-3/21
crystal symmetry operation18_466z-1/2,-x+3/2,-y+3/21
crystal symmetry operation19_563-z+1/2,-x+3/2,y-3/21
crystal symmetry operation20_556-z+1/2,x+1/2,-y+3/21
crystal symmetry operation21_354y-3/2,z+1/2,x-1/21
crystal symmetry operation22_655-y+3/2,z+1/2,-x+1/21
crystal symmetry operation23_365y-3/2,-z+3/2,-x+1/21
crystal symmetry operation24_664-y+3/2,-z+3/2,x-1/21
Buried area79600 Å2
ΔGint-1050 kcal/mol
Surface area149640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.189, 134.189, 134.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 18073.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: coaD, kdtB, yicA, b3634, JW3609 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase

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Non-polymers , 5 types, 278 molecules

#2: Chemical ChemComp-F0V / 2-benzyl-7-[(3-chloro-4-methylphenyl)amino]-5-methyl-3H-[1,2,4]triazolo[1,5-a]pyrimidin-8-ium


Mass: 364.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19ClN5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.3 M ammonium sulfate, 0.2 M potassium thiocyanate, 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→42.43 Å / Num. obs: 37868 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Rrim(I) all: 0.05 / Net I/σ(I): 39.7 / Num. measured all: 752555
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.8918.90.46254890.9720.1090.47599.9
5.66-42.4318.40.026127410.0060.02799.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.79→42.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1827 4.82 %RANDOM
Rwork0.171 ---
obs0.172 37866 100 %-
Displacement parametersBiso max: 101.84 Å2 / Biso mean: 32.23 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.79→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 85 268 2844
Biso mean--55.24 43.15 -
Num. residues----318
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d963SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes437HARMONIC5
X-RAY DIFFRACTIONt_it2756HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion354SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies15HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3787SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2756HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3752HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 1.79→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.1993 117 4.01 %
Rwork0.1804 2803 -
all0.1812 2920 -
obs--99.9 %
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)
10.9867-0.72511.34131.1059-0.31791.3164-0.0794-0.08820.05850.1096-0.0174-0.0237-0.2383-0.06870.0967-0.05940.0041-0.0006-0.1075-0.0019-0.119619.3096175.41554.6791
22.41382.55860.766700.79142.8926-0.01980.09840.0407-0.1798-0.0168-0.3182-0.0370.32180.03660.3344-0.1762-0.2841-0.01540.12610.178136.1961185.35355.6109
33.4819-0.20892.25023.4273-1.14884.6973-0.3124-0.08580.0010.4170.0316-0.1339-0.7024-0.01720.28080.14560.0245-0.0349-0.1278-0.0213-0.142623.2428182.27559.9694
42.44630.47341.92250.9985-0.44994.40860.0414-0.02740.08670.0880.00190.05290.2050.0977-0.04330.06120.02920.0018-0.0022-0.00220.033825.6574168.91856.8933
53.92620.2511-2.38215.9096-5.2167.04330.16290.2240.2436-0.456-0.04280.00610.13080.1439-0.1202-0.05360.0272-0.0241-0.0664-0.0416-0.065431.9881164.88847.7702
61.7903-2.44481.98554.505-3.38633.50960.03830.09860.0418-0.1254-0.0117-0.0423-0.04960.1146-0.0267-0.0482-0.0022-0.0116-0.0559-0.0223-0.07421.9231171.80845.923
70.6495-4.6281.59747.9984-4.00726.5892-0.0925-0.8520.02690.27790.0805-0.4150.1091-0.10730.0120.03-0.008-0.05410.0843-0.0030.13833.4514189.39142.9502
800.65260.08845.19090.099800.02790.04150.05220.6748-0.0315-0.2593-0.13570.02640.00360.089-0.0163-0.0382-0.0760.0038-0.043425.9667194.81147.0605
91.0764-0.49141.12961.3082-0.446200.0248-0.1094-0.18620.0694-0.03020.17550.0768-0.04580.0054-0.0620.0080.0059-0.0626-0.02-0.023411.7005154.68842.3415
102.1281-0.96040.1841.89660.68251.42820.09260.0655-0.30590.0305-0.10580.16690.0224-0.0730.0131-0.04480.00040.0073-0.0563-0.0010.040311.9987150.33141.476
110.5316-0.10860.58980.6415-0.26260.5637-0.0088-0.0177-0.21410.01980.02040.16740.1296-0.2352-0.0116-0.03670.01640.01150.05170.01290.06524.6814156.82941.4974
121.2085-0.132-1.42313.8856-1.62063.2445-0.22680.05930.0504-0.49230.0741-0.41740.21230.01920.15270.0158-0.01010.02330.0161-0.0279-0.000915.7749165.4437.8905
131.7481-1.26230.17720.7395-0.50520.1605-0.0872-0.04060.14060.01010.1002-0.16090.0054-0.0934-0.013-0.03220.0145-0.0309-0.0084-0.01620.019820.715159.77343.6606
145.4634-2.9814-0.34946.11592.18751.95180.08280.34040.1373-0.1953-0.0920.0777-0.1934-0.04910.0091-0.00820.0235-0.01320.0346-0.00520.043224.2095144.41730.9287
151.988-0.5753-0.28384.6356-0.31761.9313-0.06030.0936-0.1757-0.13290.02890.42150.24550.12230.0314-0.07540.0101-0.0124-0.1422-0.00360.026821.3742137.78237.1995
160.7138-0.02430.17440-0.079100.00080.00130.05150.0257-0.00490.018-0.08380.00710.00410.0269-0.04030.0755-0.0111-0.0717-0.014535.476170.91453.4752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|37 }A1 - 37
2X-RAY DIFFRACTION2{ A|38 - A|47 }A38 - 47
3X-RAY DIFFRACTION3{ A|48 - A|73 }A48 - 73
4X-RAY DIFFRACTION4{ A|74 - A|92 }A74 - 92
5X-RAY DIFFRACTION5{ A|93 - A|109 }A93 - 109
6X-RAY DIFFRACTION6{ A|110 - A|128 }A110 - 128
7X-RAY DIFFRACTION7{ A|129 - A|138 }A129 - 138
8X-RAY DIFFRACTION8{ A|139 - A|160 }A139 - 160
9X-RAY DIFFRACTION9{ B|2 - B|15 }B2 - 15
10X-RAY DIFFRACTION10{ B|16 - B|59 }B16 - 59
11X-RAY DIFFRACTION11{ B|60 - B|80 }B60 - 80
12X-RAY DIFFRACTION12{ B|81 - B|109 }B81 - 109
13X-RAY DIFFRACTION13{ B|110 - B|128 }B110 - 128
14X-RAY DIFFRACTION14{ B|129 - B|137 }B129 - 137
15X-RAY DIFFRACTION15{ B|138 - B|159 }B138 - 159
16X-RAY DIFFRACTION16{ A|201 }A201

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