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

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Basic information

Entry
Database: PDB / ID: 6cho
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with (R)-2-((1-(3-(4-methoxyphenoxy)phenyl)ethyl)amino)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one
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-F14 / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.85 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)38,28414
Polymers36,1482
Non-polymers2,13612
Water5,242291
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)114,85142
Polymers108,4436
Non-polymers6,40836
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 area25800 Å2
ΔGint-380 kcal/mol
Surface area33080 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)459,406168
Polymers433,77224
Non-polymers25,634144
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 area82600 Å2
ΔGint-1082 kcal/mol
Surface area152930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.587, 134.587, 134.587
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-F14 / 2-({(1R)-1-[3-(4-methoxyphenoxy)phenyl]ethyl}amino)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7(6H)-one


Mass: 391.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N5O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 56.51 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→38.85 Å / Num. obs: 34593 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 24.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Net I/σ(I): 31.2 / Num. measured all: 207205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.955.80.22249970.9830.1010.24499.6
5.85-38.855.70.019114310.0090.02198.7

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.85→25.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1696 4.9 %RANDOM
Rwork0.171 ---
obs0.172 34584 99.9 %-
Displacement parametersBiso max: 103.1 Å2 / Biso mean: 25.78 Å2 / Biso min: 11.29 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: 1.85→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 131 291 2934
Biso mean--35.29 37.81 -
Num. residues----320
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1004SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it2831HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies14HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3828SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2831HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3848HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion16.37
LS refinement shellResolution: 1.85→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2449 150 5.04 %
Rwork0.1916 2825 -
all0.1942 2975 -
obs--99.03 %
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)
10.2661-0.18440.92680.8629-0.38770.34380.0234-0.0776-0.06910.094-0.0463-0.07610.1119-0.07190.0229-0.03870.00190.0006-0.0211-0.0107-0.0076147.334155.92946.9647
21.63252.104-0.95851.3655-0.14521.54190.03850.2158-0.1575-0.0407-0.0768-0.0622-0.0090.02770.0383-0.00820.0522-0.02640.0665-0.0810.036145.381147.88828.195
32.3969-0.51440.52642.29980.37620.10180.0607-0.0703-0.35630.0420.04270.26120.1676-0.1295-0.1034-0.0505-0.01770.0261-0.03160.00020.0667141.8149.01142.4465
44.385-1.28050.68282.1387-0.34452.28420.0269-0.0970.1387-0.010.001-0.00930.0677-0.0428-0.028-0.02290.0093-0.0004-0.01280.00640.005143.605162.57741.5096
53.6075-0.0465-0.39491.5746-2.47591.6777-0.07240.0545-0.0385-0.2357-0.1951-0.2774-0.03550.04270.2675-0.0136-0.02320.0183-0.0201-0.0053-0.004152.079168.34334.5967
61.1611-0.62780.31891.2892-0.86580.5325-0.0417-0.10130.0869-0.0390.0332-0.2076-0.01080.02310.0086-0.0341-0.0029-0.0222-0.0355-0.0297-0.0102154.997160.29343.696
71.8332-0.232-0.38311.191-0.70610.5060.01420.0856-0.02490.01850.01930.0411-0.1508-0.1614-0.0335-0.01140.0287-0.00390.00460.00480.0024158.795144.41530.5685
81.7447-0.1413-0.01463.8429-0.47850.7283-0.05580.0317-0.20450.10970.11870.24950.26250.0481-0.06290.00420.00730.0131-0.0378-0.00240.0454155.413138.03837.8067
90.3954-1.06870.88080.59830.01930.1779-0.05-0.03510.07440.04720.01690.0177-0.121-0.10820.0331-0.0259-0.0136-0.0114-0.00330.0131-0.0305156.932175.87456.0738
101.63281.01370.56681.8841-0.24681.4047-0.0116-0.0701-0.04120.1215-0.0716-0.0281-0.22160.00830.08310.02060.0011-0.0055-0.03590.0048-0.0403158.284181.61155.3716
1100.31380.3860.33990.33920.67670.0404-0.14470.08840.15570.0026-0.0641-0.0027-0.0347-0.0430.0390.0067-0.00330.01440.010.0025159.202175.15162.0117
122.5463-1.3198-0.78413.29110.98962.52730.23140.21690.0347-0.3696-0.0472-0.2643-0.11560.0496-0.1843-0.0391-0.001-0.0009-0.0415-0.0116-0.0329163.36166.89749.8806
131.1881-1.28250.83841.5819-0.58560.37660.03370.0825-0.0162-0.13450.0068-0.0297-0.00470.0164-0.04060.0188-0.004-0.0204-0.0318-0.0098-0.0116157.016173.46945.1447
140-0.76230.08031.2518-1.00052.36360.0106-0.1587-0.1140.0321-0.0386-0.0502-0.05250.08910.0280.0174-0.0083-0.01740.03540.02190.0596167.87188.84743.5049
150.4480.39010.43061.84250.03911.1076-0.03040.03580.00210.20290.0314-0.0626-0.04640.0069-0.001-0.00010.0028-0.0022-0.08270.0077-0.0416161.002195.04846.4914
160.3722-0.56460.52760.15-0.23570.02040.0112-0.00570.0158-0.0133-0.00170.02040.0006-0.0046-0.0095-0.0099-0.0133-0.0251-0.00970.00610.02144.744160.69532.5012
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|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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