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- PDB-6chm: Phosphopantetheine adenylyltransferase (CoaD) in complex with N-(... -

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Basic information

Entry
Database: PDB / ID: 6chm
TitlePhosphopantetheine adenylyltransferase (CoaD) in complex with N-(2-(5-methoxy-1H-indol-3-yl)ethyl)pivalamide
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-F1V / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.28 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,1779
Polymers36,1482
Non-polymers1,0297
Water3,495194
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)111,53027
Polymers108,4436
Non-polymers3,08721
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 area19600 Å2
ΔGint-386 kcal/mol
Surface area33940 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)446,121108
Polymers433,77224
Non-polymers12,34884
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 area68080 Å2
ΔGint-1103 kcal/mol
Surface area146090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.386, 135.386, 135.386
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-F1V / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]-2,2-dimethylpropanamide


Mass: 274.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
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: Aug 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→39.08 Å / Num. obs: 18932 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 45.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.026 / Rrim(I) all: 0.058 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.7 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.28-2.40.31827460.9540.1630.35899.9
7.21-39.080.0186130.9990.0090.0296.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
X-Areadata reduction
PHASERphasing
RefinementResolution: 2.28→22.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.22 994 5.27 %RANDOM
Rwork0.198 ---
obs0.199 18872 99.6 %-
Displacement parametersBiso max: 118.83 Å2 / Biso mean: 42.1 Å2 / Biso min: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.28→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 65 194 2750
Biso mean--52.62 47.13 -
Num. residues----318
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d901SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes412HARMONIC5
X-RAY DIFFRACTIONt_it2627HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion340SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3347SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2627HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3569HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion15.64
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2588 159 5.29 %
Rwork0.2052 2849 -
all0.2081 3008 -
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)
11.8757-0.48070.20941.88780.00380.41340.0276-0.3746-0.08180.20450.04390.09960.0283-0.0731-0.0716-0.0835-0.00740.0138-0.0817-0.0005-0.031113.1419156.21746.0909
20.6171.88331.85751.18181.53931.0250.03830.2061-0.0045-0.0526-0.0374-0.05780.0438-0.067-0.0009-0.02760.01940.01730.1016-0.1520.238611.344149.67828.8601
33.55090.02270.23962.6104-0.67630.84910.0571-0.074-0.52850.18760.01210.29490.157-0.1152-0.0692-0.1042-0.02910.0405-0.08990.00050.12867.4737150.08742.4623
43.2095-2.06770.18633.1551-0.51980.5824-0.04950.20560.1845-0.1526-0.00760.1040.1751-0.16630.0571-0.1220.0118-0.00210.09710.01610.0078.9871163.83441.7441
54.23231.2317-2.59034.1796-1.98125.3887-0.06940.0908-0.1188-0.3022-0.063-0.1370.0781-0.19350.1325-0.0026-0.07670.0137-0.027-0.0243-0.044317.4373169.36334.7942
61.8501-1.3162-0.19231.8276-0.13581.7413-0.0308-0.0310.1512-0.02360.0825-0.0902-0.0380.0116-0.0518-0.0599-0.0333-0.0226-0.0356-0.0402-0.01220.6915161.13743.7139
70.4105-0.0653-0.05050.57970.39700.03120.0871-0.0139-0.1213-0.0333-0.02680.04210.06960.0021-0.0148-0.0041-0.02190.0073-0.00580.032524.7854144.61730.8099
81.0283-1.8349-2.32124.3395-1.13950.0538-0.047-0.1785-0.5196-0.0457-0.00560.46340.11320.33170.0525-0.04090.02140.0239-0.0842-0.03090.103821.0086139.08638.179
90.0052-2.2960.84441.99940.67591.3687-0.08460.05660.10170.1717-0.10820.1025-0.0226-0.03190.19280.0043-0.0250.0069-0.0286-0.0192-0.032122.4707176.70256.1062
102.16321.28280.05784.3795-1.44611.7431-0.011-0.0957-0.02350.4616-0.1102-0.1533-0.43280.05560.12120.0275-0.00690.0215-0.07630.0076-0.064323.8884182.5555.5108
110.02331.07691.286700.44292.33310.0696-0.15970.15430.35620.05980.0437-0.15770.0269-0.12950.1140.00480.039-0.0379-0.0156-0.022224.6424176.04361.9923
123.5095-0.3958-2.58864.12590.24036.66350.11020.07160.1675-0.28930.2351-0.3015-0.12090.1261-0.3453-0.0546-0.0353-0.0095-0.0788-0.0343-0.059728.7867167.89450.0576
133.1502-2.6040.77333.3321-0.36440-0.03560.17110.0939-0.30780.0471-0.1020.0071-0.1047-0.0115-0.0111-0.0367-0.0201-0.0479-0.0354-0.033622.5119173.62946.2495
140.02960.7001-0.1871.2666-0.88160.3929-0.01-0.0287-0.09420.0578-0.0006-0.05930.0548-0.0120.01060.0061-0.0124-0.0406-0.0066-0.00650.060433.4224190.50643.2767
150-0.2931-0.35662-0.82892.4313-0.0580.1137-0.10740.25120.062-0.0889-0.2113-0.0433-0.0040.04180.0034-0.0059-0.11960.012-0.038926.7694196.09146.4466
160.44970.2548-0.25480-0.19050.2740.00780.01760.01370.00350.03830.00470.0247-0.0217-0.0462-0.1962-0.0401-0.03370.11920.08580.077310.4863162.60433.7657
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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