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- PDB-4nat: Inhibitors of 4-Phosphopanthetheine Adenylyltransferase -

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Basic information

Entry
Database: PDB / ID: 4nat
TitleInhibitors of 4-Phosphopanthetheine Adenylyltransferase
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTransferase/transferase inhibitor / CoaD / panthetheine / Phosphopanthetheine Adenylyltransferase / CoaBC / Cytosolic / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP 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-2W5 / ADENOSINE-5'-DIPHOSPHATE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLahiri, S.D.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Discovery of Inhibitors of 4'-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy.
Authors: de Jonge, B.L. / Walkup, G.K. / Lahiri, S.D. / Huynh, H. / Neckermann, G. / Utley, L. / Nash, T.J. / Brock, J. / San Martin, M. / Kutschke, A. / Johnstone, M. / Laganas, V. / Hajec, L. / Gu, ...Authors: de Jonge, B.L. / Walkup, G.K. / Lahiri, S.D. / Huynh, H. / Neckermann, G. / Utley, L. / Nash, T.J. / Brock, J. / San Martin, M. / Kutschke, A. / Johnstone, M. / Laganas, V. / Hajec, L. / Gu, R.F. / Ni, H. / Chen, B. / Hutchings, K. / Holt, E. / McKinney, D. / Gao, N. / Livchak, S. / Thresher, J.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,22311
Polymers55,1913
Non-polymers3,0318
Water2,108117
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,44522
Polymers110,3836
Non-polymers6,06216
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area23720 Å2
ΔGint-137 kcal/mol
Surface area38520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.157, 127.283, 126.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 18397.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: coaD, MW1007 / Production host: Escherichia coli (E. coli)
References: UniProt: P63820, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-2W5 / (1R,2R)-N-(3,4-dichlorobenzyl)-2-(4,6-dimethoxypyrimidin-2-yl)cyclohexanecarboxamide


Mass: 424.321 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23Cl2N3O3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 to 19% polyethylene glycol 3350 (PEG 3350), 200 mM ammonium sulfate, 0.1M Propionic acid Cacodylate Bis-tris propane buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.72→24.92 Å / Num. obs: 55684 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.72→1.769 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→24.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.535 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 2812 5.1 %RANDOM
Rwork0.22716 ---
obs0.22966 52871 85.44 %-
all-2190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.72→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 195 117 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194027
X-RAY DIFFRACTIONr_bond_other_d0.0020.023766
X-RAY DIFFRACTIONr_angle_refined_deg2.4422.0255449
X-RAY DIFFRACTIONr_angle_other_deg1.15838716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9425464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97424.07172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50215718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0621521
X-RAY DIFFRACTIONr_chiral_restr0.2330.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1440.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8093.11856
X-RAY DIFFRACTIONr_mcbond_other2.813.0991855
X-RAY DIFFRACTIONr_mcangle_it3.6494.6252311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4543.6472171
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 68 -
Rwork0.477 1401 -
obs--30.86 %

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