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- PDB-6ckw: Phosphopantetheine adenylyltransferase (CoaD) in complex with (R)... -

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Basic information

Entry
Database: PDB / ID: 6ckw
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with (R)-3-((7-(((S)-2-amino-2-(2-methoxyphenyl)ethyl)amino)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)-3-(3-chlorophenyl)propanenitrile
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT CaaD / FBDD Gram-negative antibacterial antibiotic / Transferase Transferase-antibiotic complex / TRANSFERASE / 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-F6D / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.06 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
DepositionMar 1, 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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)38,47318
Polymers36,1482
Non-polymers2,32516
Water4,234235
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)115,41954
Polymers108,4436
Non-polymers6,97648
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area27580 Å2
ΔGint-582 kcal/mol
Surface area32990 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)461,675216
Polymers433,77224
Non-polymers27,903192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_454x-1/2,y+1/2,z-1/21
crystal symmetry operation14_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation15_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation16_445x-1/2,-y-1/2,-z+1/21
crystal symmetry operation17_445z-1/2,x-1/2,y+1/21
crystal symmetry operation18_454z-1/2,-x+1/2,-y-1/21
crystal symmetry operation19_555-z+1/2,-x+1/2,y+1/21
crystal symmetry operation20_544-z+1/2,x-1/2,-y-1/21
crystal symmetry operation21_544y+1/2,z-1/2,x-1/21
crystal symmetry operation22_445-y-1/2,z-1/2,-x+1/21
crystal symmetry operation23_555y+1/2,-z+1/2,-x+1/21
crystal symmetry operation24_454-y-1/2,-z+1/2,x-1/21
Buried area101470 Å2
ΔGint-1925 kcal/mol
Surface area140790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.330, 134.330, 134.330
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 (E. coli) / 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, 251 molecules

#2: Chemical ChemComp-F6D / (3R)-3-[(7-{[(2S)-2-amino-2-(2-methoxyphenyl)ethyl]amino}-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]-3-(3-chlorophenyl)propanenitrile


Mass: 476.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25ClN8O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
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: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→42.48 Å / Num. obs: 24939 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.041 / Net I/σ(I): 58.3 / Num. measured all: 455245
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.06-2.1718.10.11535840.9980.0280.119100
6.52-42.4816.90.02284310.0050.02299.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
PROCORdata reduction
PHASERphasing
RefinementResolution: 2.06→16.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.161 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1259 5.06 %RANDOM
Rwork0.159 ---
obs0.16 24883 99.6 %-
Displacement parametersBiso max: 103.86 Å2 / Biso mean: 22.68 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 2.06→16.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 142 235 2859
Biso mean--27.11 34.96 -
Num. residues----316
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d927SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes450HARMONIC5
X-RAY DIFFRACTIONt_it2713HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion345SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3455SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2713HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3683HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion15.45
LS refinement shellResolution: 2.06→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2019 159 5.47 %
Rwork0.1574 2750 -
all0.1598 2909 -
obs--96.47 %
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)
11.23970.0216-0.55721.1661-0.94730.90430.0461-0.10310.04480.2447-0.00240.0968-0.0272-0.005-0.0436-0.0236-0.0048-0.0074-0.0417-0.0085-0.018120.0615-13.346946.0595
22.00840.75372.91040.8214-0.93650.6474-0.01820.0908-0.1006-0.14240.14330.13680.01620.0445-0.12510.0339-0.0344-0.0316-0.03290.020.059314.375-11.693828.3452
32.2750.26780.10892.5241-0.78661.04480.0265-0.04980.21170.13440.02730.3894-0.1881-0.1518-0.0538-0.03090.01510.0156-0.0731-0.03860.074314.2849-7.44542.5869
42.3252-0.5769-0.28782.9970.41371.18090.0593-0.12070.19880.2659-0.01850.0559-0.10290.0127-0.04080.0049-0.0144-0.0028-0.0511-0.0109-0.011227.886-8.986441.9664
53.73690.9594-1.10582.8593-2.7752.10840.05430.2017-0.2165-0.0197-0.02440.0648-0.14260.0623-0.0299-0.00650.0220.01090.0179-0.017-0.025633.8023-17.200534.9854
62.23931.5659-0.04621.6290.25710.35270.0073-0.07440.02320.0681-0.01540.0129-0.04520.09780.0080.00280.0097-0.0301-0.01090.0064-0.001225.6985-20.524443.6438
70.17580.39241.17031.24821.39410.21310.00480.0338-0.02180.0947-0.04430.0177-0.06120.00070.0395-0.03930.0178-0.0053-0.0260.0065-0.00888.9036-24.869330.5587
84.65330.26460.3071.1254-0.55590.133-0.0377-0.09090.32920.08250.00140.23120.0503-0.180.0363-0.04350.0080.02260.00070.00070.05973.5064-21.288538.177
91.67210.7414-0.73770-0.23981.6728-0.0075-0.03420.01830.0785-0.12110.0058-0.14670.03450.12860.00560.02290.0053-0.0221-0.0032-0.031841.8159-22.861455.7124
102.2641-0.9126-0.70241.9907-0.07252.063-0.0922-0.14050.02540.1180.00620.0343-0.08930.19920.086-0.0288-0.0114-0.01120.0047-0.0088-0.060946.6694-23.475155.378
110.0006-1.381-0.54030.2382-1.12332.6362-0.029-0.22220.03780.1294-0.0398-0.0303-0.2435-0.02010.0688-0.00050.0135-0.01690.0172-0.0205-0.020240.3259-23.927361.8243
121.8615-0.4793-0.23360.96430.47712.14670.03220.1774-0.02810.02080.06560.06090.08290.0447-0.0978-0.02240.0142-0.0133-0.0259-0.004-0.035132.3277-28.426550.3041
131.8282-0.2589-1.25670.6743-0.08010.72240.02310.09010.0877-0.0518-0.00090.0320.0063-0.0093-0.0223-0.00230.008-0.01320.025-0.0082-0.02137.0191-22.549647.0686
141.1293-1.67510.96430-0.44710.72620.0004-0.0277-0.05330.01970.0349-0.0389-0.0519-0.079-0.03530.0153-0.0088-0.02120.0150.0178-0.007855.1058-32.940143.0333
152.381-1.23-0.0341.19-0.15172.75190.0149-0.22870.1372-0.0802-0.0179-0.187-0.04660.1260.003-0.0623-0.0266-0.00360.01560.0045-0.001960.4408-26.190146.2968
160.09760.79590.12231.02490.30340-0.0216-0.01860.0090.01730.0088-0.004-0.061-0.06750.0128-0.01080.00810.0305-0.02770.00720.039326.9251-11.07830.9431
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|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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