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

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Basic information

Entry
Database: PDB / ID: 6chp
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with methyl (R)-4-(3-(2-cyano-1-((5-methyl-1H-imidazo[4,5-b]pyridin-2-yl)amino)ethyl)benzyl)piperidine-1-carboxylate
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / Dephospho-CoA pyrophosphorylase Pantetheine-phosphate adenylyltransferase PPAT CaaD / FBDD Gram-negati Pantetheine-phosphate adenylyltransferaseve 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-F0Y / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 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: 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)38,07612
Polymers36,1482
Non-polymers1,92810
Water4,342241
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)114,22736
Polymers108,4436
Non-polymers5,78430
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 area23120 Å2
ΔGint-357 kcal/mol
Surface area34050 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)456,909144
Polymers433,77224
Non-polymers23,136120
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 area78020 Å2
ΔGint-1079 kcal/mol
Surface area150670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.634, 135.634, 135.634
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-412-

HOH

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Components

#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
#2: Chemical ChemComp-F0Y / methyl 4-[(3-{(1R)-2-cyano-1-[(5-methyl-3H-imidazo[4,5-b]pyridin-2-yl)amino]ethyl}phenyl)methyl]piperidine-1-carboxylate


Mass: 432.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28N6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
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: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→42.89 Å / Num. obs: 30962 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.018 / Rrim(I) all: 0.058 / Net I/σ(I): 27.2 / Num. measured all: 334792
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.94-2.0410.80.20644770.990.0650.216100
6.12-42.8910.20.02810400.9990.0090.02998.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
X-Areadata reduction
PHASERphasing
RefinementResolution: 1.94→24.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1544 5.01 %RANDOM
Rwork0.168 ---
obs0.169 30793 100 %-
Displacement parametersBiso max: 95.02 Å2 / Biso mean: 27.89 Å2 / Biso min: 13.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.94→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 119 241 2848
Biso mean--37.24 40.68 -
Num. residues----318
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d997SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it2810HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion359SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies16HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3558SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2810HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3821HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion15.49
LS refinement shellResolution: 1.94→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2239 154 5.15 %
Rwork0.1969 2835 -
all0.1984 2989 -
obs--100 %
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)
10.54460.16411.38741.447-0.59430.01580.0491-0.1819-0.06150.1694-0.0389-0.06220.0915-0.0701-0.0102-0.0325-0.00080.0115-0.0118-0.0177-0.002213.1837156.6946.2992
21.71520.9055-0.50511.04030.86410.80220.0480.115-0.1599-0.084-0.0648-0.0731-0.0107-0.02770.0168-0.01130.0707-0.01120.0149-0.05310.009611.4109149.70428.5757
33.1921-0.2672-0.07082.29190.04970.25770.0316-0.1455-0.45830.03790.03380.23440.1694-0.0855-0.0655-0.0516-0.01180.0209-0.02910.00230.05957.5463150.23442.7016
44.0753-1.78810.61051.69580.14711.78550.00530.04740.2382-0.08860.0356-0.00550.0909-0.1006-0.0409-0.0528-0.00120.00530.01780.02730.00269.2168163.74341.3343
54.48360.5820.98961.535-2.32493.1087-0.0473-0.11970.028-0.2986-0.1145-0.20780.0062-0.06820.1618-0.0224-0.07210.01440.0001-0.0221-0.034517.0837170.21234.7779
60.0227-0.2904-0.74840.3843-0.31040.4727-0.0192-0.01740.0753-0.1399-0.0125-0.10810.01340.02860.0317-0.04480.0073-0.0539-0.0127-0.05940.028321.0988161.4444.1201
71.1949-0.9883-1.98070.747-0.0270.06240.00970.0030.0261-0.0624-0.06890.0424-0.0556-0.05580.0593-0.00910.0229-0.0074-0.01230.00570.02924.7313145.3331.0188
80.6671-0.9653-0.48884.3537-0.16940.4478-0.04130.0171-0.21770.11580.050.21740.220.073-0.0087-0.01230.00590.0126-0.04270.0030.049421.0927139.28838.4623
90.088-1.69220.60260.40540.09871.1074-0.02010.00270.08030.0233-0.01540.0625-0.0081-0.05450.03550.0045-0.029-0.0121-0.0180.0043-0.027323.4703177.73255.9947
101.75070.87510.46272.557-0.5841.7952-0.0249-0.0635-0.08820.1127-0.074-0.0784-0.171-0.03820.09890.00650.0099-0.0012-0.0513-0.005-0.056623.6167183.07155.8536
110.39910.19750.8820.56730.7271.62850.024-0.07210.14640.26890.0185-0.07330.0953-0.0392-0.04260.06570.00480.0070.00350.0094-0.003324.7486176.53462.3776
121.9411-0.5885-1.16543.63810.4222.50660.08030.07620.0326-0.26410.1128-0.2820.01550.0313-0.193-0.0699-0.0209-0.0099-0.0532-0.0286-0.036228.8162168.43650.2163
130.069-1.34260.29743.4229-1.46450.90350.03450.0638-0.0215-0.24040.0236-0.1101-0.048-0.0282-0.05810.0252-0.0248-0.00560.0055-0.0053-0.004422.8413174.96845.6333
140.27461.35130.09170.393-0.78741.90220-0.0722-0.0961-0.0141-0.0501-0.0105-0.0050.08610.050.014-0.0040.0014-0.0037-0.01130.042433.5274190.69743.7029
150.63150.55840.31752.3084-0.39682.0296-0.08680.0457-0.06490.2470.1065-0.1021-0.0877-0.0639-0.01970.01230.0064-0.0034-0.08770.005-0.030326.6783196.70346.7467
160.34420.6631-0.678200.27320.28260.00830.0037-0.0819-0.0108-0.0419-0.0096-0.05560.02640.0337-0.0444-0.03370.003-0.01460.05690.060410.1541162.13132.9212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|37 }A2 - 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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