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- PDB-6chn: Phosphopantetheine adenylyltransferase (CoaD) in complex with met... -

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Basic information

Entry
Database: PDB / ID: 6chn
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with methyl (R)-4-(3-(2-cyano-1-((5-methyl-7-oxo-4,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)ethyl)phenoxy)piperidine-1-carboxylate
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / 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-F1D / DI(HYDROXYETHYL)ETHER / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.03 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,02612
Polymers36,1482
Non-polymers1,87810
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)114,07736
Polymers108,4436
Non-polymers5,63430
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation9_654y+1,z,x-11
Buried area21660 Å2
ΔGint-353 kcal/mol
Surface area34250 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)456,306144
Polymers433,77224
Non-polymers22,534120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation6_665z+1,-x+1,-y1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_645-z+1,x-1,-y1
crystal symmetry operation9_654y+1,z,x-11
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_656y+1,-z,-x+11
crystal symmetry operation12_654-y+1,-z,x-11
crystal symmetry operation13_444x-1/2,y-1/2,z-1/21
crystal symmetry operation14_754-x+5/2,-y+1/2,z-1/21
crystal symmetry operation15_745-x+5/2,y-1/2,-z+1/21
crystal symmetry operation16_455x-1/2,-y+1/2,-z+1/21
crystal symmetry operation17_534z+1/2,x-3/2,y-1/21
crystal symmetry operation18_565z+1/2,-x+3/2,-y+1/21
crystal symmetry operation19_664-z+3/2,-x+3/2,y-1/21
crystal symmetry operation20_635-z+3/2,x-3/2,-y+1/21
crystal symmetry operation21_543y+1/2,z-1/2,x-3/21
crystal symmetry operation22_646-y+3/2,z-1/2,-x+3/21
crystal symmetry operation23_556y+1/2,-z+1/2,-x+3/21
crystal symmetry operation24_653-y+3/2,-z+1/2,x-3/21
Buried area72010 Å2
ΔGint-1091 kcal/mol
Surface area151620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.804, 134.804, 134.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

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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-F1D / methyl 4-(3-{(1R)-2-cyano-1-[(5-methyl-7-oxo-6,7-dihydro[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]ethyl}phenoxy)piperidine-1-carboxylate


Mass: 451.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N7O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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: 2.84 Å3/Da / Density % sol: 56.72 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→42.63 Å / Num. obs: 26447 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 24.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.014 / Rrim(I) all: 0.045 / Net I/σ(I): 39.4 / Num. measured all: 271760
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.1410.10.15138400.9930.050.15999.3
6.42-42.639.70.02489310.0080.02599.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
X-Areadata reduction
PHASERphasing
RefinementResolution: 2.03→24.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1298 4.91 %RANDOM
Rwork0.163 ---
obs0.165 26420 100 %-
Displacement parametersBiso max: 95.88 Å2 / Biso mean: 24.27 Å2 / Biso min: 10.59 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: 2.03→24.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 118 268 2872
Biso mean--32.99 38.11 -
Num. residues----317
LS refinement shellResolution: 2.03→2.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2236 112 3.8 %
Rwork0.1658 2836 -
all0.1679 2948 -
obs--99.97 %
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)
100.28241.14581.79660.18630.24690.0452-0.1247-0.03420.1227-0.0379-0.05840.0706-0.0019-0.0073-0.0376-0.00450.018-0.0136-0.0039-0.0024147.95720.793145.8188
20.41161.449-0.99790.78971.14581.02280.03620.1776-0.1019-0.0469-0.0906-0.0685-0.0142-0.00360.05440.00010.065-0.0280.0416-0.03350.0029145.75813.525928.1637
33.2085-0.71510.24222.1901-0.37181.0108-0.0064-0.1296-0.4402-0.04180.02720.23150.2129-0.1046-0.0209-0.0565-0.02380.0243-0.036-0.00060.0801142.26114.130842.217
43.7153-1.37671.06272.27510.09340.8334-0.0080.02450.2125-0.0878-0.00430.00720.0785-0.10790.0123-0.06060.01810.01350.04090.0298-0.0085143.77728.222941.2151
55.34091.47070.82840.0016-2.05033.5849-0.026-0.0118-0.1252-0.2877-0.062-0.11350.0571-0.03640.088-0.021-0.04810.0258-0.0406-0.0204-0.0335152.1234.129334.6686
60.00620.3447-0.65720.2536-0.00930.6812-0.011-0.02840.0686-0.02680.0126-0.11760.01740.0961-0.0016-0.02540.0047-0.03470.0027-0.04640.0216156.4724.903543.4253
70.65960.7078-1.23130.88710.78360-0.0030.02510.0763-0.0467-0.04080.0111-0.1249-0.01320.0438-0.02650.0279-0.00390.00510.0151-0.0173159.1929.995730.6771
80.5233-0.7202-0.47165.07180.1660.1173-0.01130.0264-0.19590.12340.00370.24330.23810.08770.0076-0.00280.01150.0179-0.02350.01310.0437155.7243.445438.0711
90-1.13980.23381.1529-0.78091.7168-0.02470.00150.05410.0134-0.0088-0.00160.0049-0.09590.0336-0.0044-0.0151-0.0108-0.02070.0094-0.0261157.67941.475855.9679
102.06480.49530.57082.1531-0.67252.18430.01480.0072-0.02850.1061-0.0942-0.0231-0.1741-0.00090.07940.00740.01150.01-0.05480.002-0.0553158.5347.297655.4354
110.4070.15010.74710.94711.11192.27270.045-0.09830.10790.35290.0632-0.11110.1706-0.0646-0.10820.0684-0.0092-0.0029-0.01980.01160.0014159.29940.400561.951
121.0588-0.3902-0.91673.73940.62210.74350.04080.01810.0978-0.21780.1218-0.32880.10420.0314-0.1626-0.0715-0.0097-0.0101-0.0359-0.017-0.0234163.27732.546750.0842
130.6793-1.031-0.07532.4793-0.70950.38310.00810.12980.0519-0.20680.0349-0.0933-0.1206-0.0349-0.0430.0069-0.0182-0.00470.0088-0.0133-0.0059157.28438.720445.3684
1401.13470.57590.3324-0.34831.52070.0003-0.0628-0.07240.0251-0.0371-0.0155-0.01070.07220.03680.00280.00620.0039-0.00280.00370.0428168.16954.255443.4855
151.0671.226-0.13122.2334-0.98491.3281-0.07350.0214-0.02210.31470.0816-0.0271-0.105-0.101-0.00810.01420.01860.0017-0.08670.0086-0.0259161.38960.637246.3939
160.34710.1822-0.4370.13390.39790.11140.00510.0174-0.0428-0.0062-0.0225-0.0011-0.00520.0010.0174-0.029-0.0322-0.0230.00070.03510.0298144.88326.316232.4623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|37 }A3 - 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|159 }A139 - 159
9X-RAY DIFFRACTION9{ B|1 - B|15 }B1 - 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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