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- PDB-5ifi: CRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOS... -

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Basic information

Entry
Database: PDB / ID: 5ifi
TitleCRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOSINE-5'-PROPYLPHOSPHATE FROM CRYPTOCOCCUS NEOFORMANS H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / NIH / NIAID / SBRI / UW / BERYLLIUM / SYNTHETASE / ACS1 / PRX / PROPYL-AMP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / SSGCID / Fox III, D. / Edwards, T.E. / Lorimer, D.D. / Mutz, M.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: Synthesis and evaluation of acyl-AMP phosphate isosteres as inhibitors of fungal acetyl CoA synthetase.
Authors: Daraji, D.G. / Jezewski, A.J. / Alden, K.M. / Propp, J.P. / Heene, M.E. / Soldan, C.A. / Liu, L. / Battaile, K.P. / Lovell, S. / Staker, B.L. / Krysan, D.J. / Hagen, T.J.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 10, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,09228
Polymers232,4273
Non-polymers2,66525
Water17,457969
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,48612
Polymers77,4761
Non-polymers1,01011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,61712
Polymers77,4761
Non-polymers1,14211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9894
Polymers77,4761
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.460, 185.550, 84.890
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_00797 / Plasmid: PEMB7013 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Chemical ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H20N5O7P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ...Details: ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ADENOSINE-5'- PROPYLPHOSPHATE AND COA WERE ADDED TO THE PROTEIN SOLUTION AND INCUBATED FOR 5 MINUTES BEFORE SETTING UP TRIALS. CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND IN WIZARD 1 AND 2 SCREEN CONDITION E8 (10% W/V PEG8,000, 0.1M NA/K PHOSPHATE PH6.2) AND CRYO-PROTECTED IN 20% ETHYLENE GLYCOL. CRYSTAL ID 269918E8 DIT9-1 APS 21-ID-F), PH 6.20, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 159980 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 34.78 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.96
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.47 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(DEV_2328: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RY2

1ry2


Resolution: 1.95→41.84 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.213 8023 5.02 %
Rwork0.185 --
obs0.186 159842 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14105 0 170 969 15244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614805
X-RAY DIFFRACTIONf_angle_d0.79120220
X-RAY DIFFRACTIONf_dihedral_angle_d14.5068642
X-RAY DIFFRACTIONf_chiral_restr0.1442194
X-RAY DIFFRACTIONf_plane_restr0.0062614
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)
11.25110.03420.21130.92620.13811.14760.13040.015-0.1069-0.33630.26250.57320.1061-0.6293-0.07610.1225-0.0933-0.09950.60310.25330.5981-33.60836.9727-16.1587
21.1019-0.72320.47282.3643-0.57161.00840.10960.1476-0.0499-0.3613-0.0290.07350.24890.1077-0.10180.18590.01810.00950.262-0.0130.1575-2.6446-5.4534-11.1736
31.2534-0.50190.55571.6402-0.69251.18270.19280.1851-0.2024-0.49610.06640.38230.4472-0.0838-0.16010.3152-0.0276-0.09340.2868-0.00410.239-13.5203-7.8192-18.2454
40.81510.22570.41092.1855-0.6751.29280.03350.00620.0201-0.17980.07910.27390.0189-0.1456-0.08950.13020.01270.010.3020.04570.2607-17.495113.8927-19.349
51.50960.21120.70152.13621.0022.30280.07410.3989-0.1062-0.78780.15750.22040.16210.1806-0.21120.6133-0.0117-0.16510.51780.06390.3815-20.04797.9049-41.9767
60.8674-0.54950.06251.21340.77180.8214-0.1118-0.3068-0.30861.00620.49390.2677-0.1278-0.28850.5180.71910.13880.33510.39720.15470.3029-0.2872-30.499238.1783
70.4828-0.5841-0.02061.8885-0.61090.9203-0.1399-0.07280.08530.5440.15450.1064-0.1461-0.06910.00120.33660.0790.06760.2519-0.00610.16334.4607-9.778921.3873
82.18-0.49650.2991.9084-0.25721.1151-0.13690.1190.2240.2672-0.0229-0.4912-0.03250.25560.13910.22110.0136-0.06940.28110.03420.292526.754-9.293214.379
91.91280.47120.03841.4808-1.02652.39-0.1177-0.0419-0.0830.39150.16140.0673-0.03750.02380.05270.22460.07090.07050.19710.00640.13858.3654-17.125416.5396
100.15180.0170.37751.4611-0.47661.2298-0.247-0.1240.08571.05180.1063-0.2763-0.27290.04980.1180.59510.0942-0.09710.28120.00010.205418.42-18.724932.2962
111.347-0.04520.31961.4411-0.05351.3505-0.174-0.3137-0.17331.09210.1756-0.2102-0.20290.04220.01510.6960.0842-0.0510.2990.0550.263917.9698-31.873238.899
120.8613-0.49290.63282.3176-1.41362.27050.0162-0.1181-0.20940.00520.16730.44950.2506-0.2528-0.20910.28040.00960.07810.22540.02450.26491.7467-30.673117.6869
132.6906-0.58440.87845.14290.26491.85660.04860.0775-0.2218-0.08030.23110.1038-0.1562-0.0122-0.19840.3596-0.00550.06810.23980.02570.243810.3048-45.185124.2368
143.68330.12260.9455.78570.27573.0074-0.01110.1122-0.2850.28780.1941-0.69950.02670.1095-0.34030.29590.00580.0010.2262-0.04490.393321.3881-54.181328.4186
151.99640.76640.26131.5541-1.00651.4657-0.04480.53840.0273-0.64110.2994-0.8719-1.02140.5704-0.25380.8047-0.21360.30920.5671-0.17720.668624.4402-45.974420.24
160.71890.2737-0.4020.51630.17030.5335-0.3151-0.61370.38340.93330.1379-0.2064-0.5855-0.22930.11270.85680.1585-0.20680.4478-0.16610.38925.94820.238325.0709
170.5589-0.13710.04050.85240.00841.3283-0.33270.22790.48190.23770.0132-0.3582-0.6816-0.11450.21980.37880.045-0.15870.24290.03170.49213.945130.92930.9624
181.2112-0.35380.03570.2272-0.07681.1852-0.22250.33560.53970.2291-0.1779-0.5336-0.34130.25860.23350.1849-0.0804-0.09910.34880.19340.581718.477821.8391-5.2477
190.32840.21160.5181.5153-0.56451.4716-0.3686-0.12390.66550.6888-0.0533-0.4271-0.66720.07130.26070.56740-0.27650.2749-0.04190.589913.386326.856712.6466
200.10310.18410.10610.8738-0.28880.626-0.2984-0.03880.78560.6243-0.1209-0.2513-1.08740.22230.00731.1346-0.0408-0.65090.08330.06181.209614.086646.33177.4546
210.4707-0.0719-0.26781.25850.32951.5845-0.1266-0.19250.72490.3267-0.0982-0.2853-1.06050.06230.21681.2167-0.0098-0.55920.3747-0.19521.020516.961739.989520.9378
221.16910.3053-0.81141.49510.3830.808-0.3051-0.56450.56060.4383-0.0585-0.3149-0.64740.06140.14841.25690.0789-0.51750.569-0.23420.853921.07231.060633.9102
231.13910.80020.22851.3678-0.11810.128-0.1764-0.43270.48060.5641-0.15-0.4077-0.6320.17920.04960.7974-0.0193-0.41090.4241-0.05960.669124.92422.562825.9375
248.30730.1353-5.16492.45642.58666.11630.2121-0.02971.2212-0.38810.182-0.1496-0.57290.1059-0.27990.80090.1411-0.07020.8480.00611.164341.897431.587812.4425
255.55041.48081.1313.9626-0.21793.7704-0.124-0.00031.5615-0.38750.16980.091-0.02490.6238-0.13030.63830.07370.01230.90340.10321.22444.725135.47736.0089

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