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

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Basic information

Entry
Database: PDB / ID: 6chl
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with (R)-3-(3-chlorophenyl)-3-((5-methyl-7-oxo-4,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)propanenitrile
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-EXJ / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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)37,55612
Polymers36,1482
Non-polymers1,40810
Water3,351186
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)112,66736
Polymers108,4436
Non-polymers4,22430
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation9_564y,z+1,x-11
Buried area21250 Å2
ΔGint-479 kcal/mol
Surface area33710 Å2
MethodPISA
2
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)450,669144
Polymers433,77224
Non-polymers16,897120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_674-z+1,-x+2,y-11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_766-y+2,z+1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation13_444x-1/2,y-1/2,z-1/21
crystal symmetry operation14_774-x+5/2,-y+5/2,z-1/21
crystal symmetry operation15_745-x+5/2,y-1/2,-z+1/21
crystal symmetry operation16_475x-1/2,-y+5/2,-z+1/21
crystal symmetry operation17_543z+1/2,x-1/2,y-3/21
crystal symmetry operation18_576z+1/2,-x+5/2,-y+3/21
crystal symmetry operation19_673-z+3/2,-x+5/2,y-3/21
crystal symmetry operation20_646-z+3/2,x-1/2,-y+3/21
crystal symmetry operation21_453y-1/2,z+1/2,x-3/21
crystal symmetry operation22_756-y+5/2,z+1/2,-x+3/21
crystal symmetry operation23_466y-1/2,-z+3/2,-x+3/21
crystal symmetry operation24_763-y+5/2,-z+3/2,x-3/21
Buried area77340 Å2
ΔGint-1524 kcal/mol
Surface area142510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.837, 134.837, 134.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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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-EXJ / (3R)-3-(3-chlorophenyl)-3-[(5-methyl-7-oxo-6,7-dihydro[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]propanenitrile


Mass: 328.756 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13ClN6O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
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: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→42.64 Å / Num. obs: 20787 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 38.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.023 / Rrim(I) all: 0.05 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.324.50.18829840.9740.0990.21399.4
6.96-42.644.40.027080.9990.0110.02399

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.2→38.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.231 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1059 5.1 %RANDOM
Rwork0.187 ---
obs0.188 20785 99.8 %-
Displacement parametersBiso max: 123.25 Å2 / Biso mean: 37.92 Å2 / Biso min: 18.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.2→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 85 186 2747
Biso mean--52.26 44.54 -
Num. residues----317
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d898SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes431HARMONIC5
X-RAY DIFFRACTIONt_it2655HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
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_contact3350SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2655HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3614HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion15.5
LS refinement shellResolution: 2.2→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2271 138 4.62 %
Rwork0.1967 2846 -
all0.1981 2984 -
obs--99.37 %
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)
11.7091-0.76911.30621.4229-0.26921.3903-0.0733-0.1941-0.09470.21750.04480.1507-0.237-0.25510.0284-0.0119-0.0060.0194-0.03010.009-0.0705154.73177.10354.3594
22.00640.1346-1.38350-2.84580-0.01780.0065-0.0363-0.0539-0.0117-0.1292-0.08410.17020.02950.1541-0.0991-0.0793-0.00160.0151-0.0212171.371186.16455.9845
31.1064-0.11381.90682.7549-0.16464.53580.0257-0.2405-0.0490.4042-0.05820.0452-0.5442-0.16890.03250.13920.01270.0022-0.0796-0.0033-0.1167158.031183.35960.1634
42.93781.5822.10884.9941.16694.56180.0608-0.07980.00630.4925-0.0121-0.07270.1949-0.0085-0.04870.00750.02370.0142-0.07150.0142-0.0238160.133169.88457.261
55.14440.8394-2.4592.8126-2.18111.96690.00320.22060.1049-0.16910.06080.08530.08840.2818-0.064-0.04380.0158-0.0241-0.048-0.091-0.0056166.999165.64748.4426
62.2259-2.8811.35373.0435-0.85990.6257-0.02780.1910.0302-0.1545-0.0189-0.1029-0.0627-0.01180.04680.0269-0.0247-0.0211-0.0336-0.0173-0.0257156.68173.22245.7967
70.4584-2.88742.52711.8071-2.88350.4006-0.0297-0.20350.02460.02830.0667-0.11510.05160.1568-0.037-0.0216-0.0017-0.02730.0673-0.05940.031168.394190.58142.8579
80.74780.9973-0.52253.5058-0.17021.2229-0.02390.13940.03410.5230.027-0.0379-0.2801-0.1028-0.00310.1090.0008-0.0229-0.12070.0028-0.0519160.812195.86247.3397
91.4267-0.6860.03350.4433-0.92190.03210.0301-0.2604-0.0713-0.0032-0.00470.0653-0.0539-0.1584-0.0253-0.0170.0318-0.0037-0.0278-0.05430.0005147.156154.98142.1044
103.5355-1.6724-0.04562.89231.9823.58920.0582-0.0218-0.44790.0621-0.14010.2276-0.0256-0.19490.0819-0.1062-0.01860.0151-0.1098-0.00460.0397147.126150.93541.914
112.83850.2021-0.59321.71880.68532.4896-0.0114-0.1862-0.3380.02620.02370.12870.0586-0.0923-0.0122-0.0834-0.0210.01240.0079-0.00770.1261140.17156.77842.682
122.6626-0.5328-2.1615.3416-1.13113.6395-0.10760.1394-0.0162-0.48560.1654-0.46360.0018-0.2054-0.0579-0.05-0.03850.0136-0.0598-0.0596-0.0601150.469166.27738.3007
130.1826-1.16120.16912.0625-0.92970.7383-0.01910.07950.0498-0.10280.0952-0.1353-0.0770.0942-0.0761-0.0222-0.0163-0.0451-0.0194-0.04710.0606155.498160.62643.8263
141.7379-0.31-0.28260.23852.22010.3054-0.01710.0191-0.0286-0.0833-0.095-0.0510.05710.10370.1121-0.01090.014-0.02070.02180.00240.0654159.208145.01831.0785
151.2382-0.4781-0.38926.79680.1521.6246-0.00540.0167-0.34510.0133-0.0050.50060.2850.20310.0104-0.08110.0056-0.0225-0.0968-0.00160.0965156.521138.42237.3611
160-0.0970.09360.120.0950.2570.00430.0435-0.02780.0053-0.0263-0.0166-0.0388-0.01390.0220.05250.0143-0.027-0.0768-0.08530.0263169.7173.49156.6637
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|160 }A139 - 160
9X-RAY DIFFRACTION9{ B|3 - B|15 }B3 - 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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