PDB-9cd8: Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neof...

ID or keywords:

Entry

Database: PDB / ID: 9cd8

Title

Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neoformans H99 in complex with inhibitor HGN-1310 (dd3-027)

Components

(Acetyl-coenzyme A ...) x 2

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Acetyl-coenzyme A synthetase 2

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

Biological species

Cryptococcus neoformans var. grubii (Cryptococcus neoformans serotype A)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: Nat Commun / Year: 2025
Title: Discovery and mechanism of a highly selective, antifungal acetyl-CoA synthetase inhibitor.
Authors: Jezewski, A.J. / Alden, K.M. / Propp, J. / Daraji, D.G. / Lail 3rd, C.L. / Heene, M.E. / Fuller, A.J. / Ferreira, J.C. / Liu, L. / Battaile, K.P. / Williams, N.S. / Staker, B.L. / Lovell, S. ...

History

Deposition	Jun 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9cd8.cif.gz	747.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9cd8.ent.gz		Display	PDB format
PDBx/mmJSON format	9cd8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9cd8_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9cd8_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9cd8_validation.xml.gz	78.5 KB	Display
Data in CIF	9cd8_validation.cif.gz	102.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cd/9cd8 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/9cd8	HTTPS FTP

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Related structure data

Related structure data	8g0tC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (6)

Deposited unit

A: Acetyl-coenzyme A synthetase

B: Acetyl-coenzyme A synthetase

C: Acetyl-coenzyme A synthetase

hetero molecules

235 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	176.224, 176.224, 159.461
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-828- HOH

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Acetyl-coenzyme A ... , 2 types, 3 molecules ABC

#1: Protein	Acetyl-coenzyme A synthetase Mass: 77516.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The ALY modified LYS residues was modeled in chain A only. Source: (gene. exp.) Cryptococcus neoformans var. grubii (Cryptococcus neoformans serotype A) Gene: CNAG_00797 / Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Protein	Acetyl-coenzyme A synthetase Mass: 77475.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii (Cryptococcus neoformans serotype A) Gene: CNAG_00797 / Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase

#1: Protein

Acetyl-coenzyme A synthetase

Mass: 77516.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The ALY modified LYS residues was modeled in chain A only.
Source: (gene. exp.)

Cryptococcus neoformans var. grubii (Cryptococcus neoformans serotype A)
Gene: CNAG_00797 / Plasmid: CrneC.00629.a.FS11 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase

#2: Protein

Acetyl-coenzyme A synthetase

Mass: 77475.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cryptococcus neoformans var. grubii (Cryptococcus neoformans serotype A)
Gene: CNAG_00797 / Plasmid: CrneC.00629.a.FS11 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase

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Non-polymers , 5 types, 565 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-A1AV1 / (5P)-3-azido-N-[(5-cyclopropyl-1,2-oxazol-3-yl)methyl]-5-(2,3-dihydro-1-benzofuran-5-yl)-N-methylbenzamide Mass: 415.445 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₃H₂₁N₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.81 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Index F8: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1310 (dd3-027) inhibitor added to the protein prior ...Details: Index F8: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1310 (dd3-027) inhibitor added to the protein prior to crystallization. Plate: 13756 well F8 drop 2. Puck: PSL-1509, Cryo: 20% glycerol + 80% crystallant

Crystal

Density Matthews: 2.66 Å³/Da / Density % sol: 53.81 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Index F8: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1310 (dd3-027) inhibitor added to the protein prior ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 19, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.4→176.22 Å / Num. obs: 98167 / % possible obs: 100 % / Redundancy: 13 % / CC_1/2: 0.998 / R_merge(I) obs: 0.177 / R_pim(I) all: 0.051 / R_rim(I) all: 0.184 / Χ²: 1 / Net I/σ(I): 13 / Num. measured all: 1273162
Reflection shell	Resolution: 2.4→2.46 Å / % possible obs: 100 % / Redundancy: 13.5 % / R_merge(I) obs: 1.854 / Num. measured all: 96895 / Num. unique obs: 7166 / CC_1/2: 0.663 / R_pim(I) all: 0.523 / R_rim(I) all: 1.927 / Χ²: 0.99 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5177	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→124.61 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2192	4864	4.96 %
R_work	0.1785	-	-
obs	0.1805	98069	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.4→124.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14436	0	159	548	15143

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	15056
X-RAY DIFFRACTION	f_angle_d	0.603	20506
X-RAY DIFFRACTION	f_dihedral_angle_d	12.541	5432
X-RAY DIFFRACTION	f_chiral_restr	0.046	2182
X-RAY DIFFRACTION	f_plane_restr	0.006	2647

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.43	0.3517	162	0.2995	3078	X-RAY DIFFRACTION	100
2.43-2.46	0.331	153	0.2808	3042	X-RAY DIFFRACTION	100
2.46-2.49	0.3263	153	0.2564	3106	X-RAY DIFFRACTION	100
2.49-2.52	0.3184	171	0.2421	3023	X-RAY DIFFRACTION	100
2.52-2.55	0.2709	178	0.2276	3072	X-RAY DIFFRACTION	100
2.55-2.59	0.26	160	0.2183	3044	X-RAY DIFFRACTION	100
2.59-2.62	0.2691	157	0.2096	3078	X-RAY DIFFRACTION	100
2.62-2.66	0.2676	147	0.1999	3085	X-RAY DIFFRACTION	100
2.66-2.7	0.2784	149	0.1971	3095	X-RAY DIFFRACTION	100
2.7-2.75	0.2358	151	0.2058	3074	X-RAY DIFFRACTION	100
2.75-2.79	0.2572	153	0.2095	3100	X-RAY DIFFRACTION	100
2.79-2.85	0.2466	179	0.2086	3065	X-RAY DIFFRACTION	100
2.85-2.9	0.2455	164	0.2228	3079	X-RAY DIFFRACTION	100
2.9-2.96	0.2641	165	0.2376	3055	X-RAY DIFFRACTION	100
2.96-3.02	0.2858	146	0.24	3098	X-RAY DIFFRACTION	100
3.02-3.09	0.2858	169	0.2252	3077	X-RAY DIFFRACTION	100
3.09-3.17	0.251	151	0.206	3108	X-RAY DIFFRACTION	100
3.17-3.26	0.2064	175	0.1888	3094	X-RAY DIFFRACTION	100
3.26-3.35	0.201	160	0.1759	3087	X-RAY DIFFRACTION	100
3.35-3.46	0.2317	148	0.1783	3115	X-RAY DIFFRACTION	100
3.46-3.58	0.2287	156	0.177	3087	X-RAY DIFFRACTION	100
3.59-3.73	0.232	156	0.1842	3124	X-RAY DIFFRACTION	100
3.73-3.9	0.2196	174	0.1672	3127	X-RAY DIFFRACTION	100
3.9-4.1	0.1776	184	0.1444	3092	X-RAY DIFFRACTION	100
4.1-4.36	0.154	155	0.1288	3121	X-RAY DIFFRACTION	100
4.36-4.7	0.1623	138	0.1258	3173	X-RAY DIFFRACTION	100
4.7-5.17	0.1702	157	0.1248	3180	X-RAY DIFFRACTION	100
5.17-5.92	0.1962	205	0.149	3136	X-RAY DIFFRACTION	100
5.92-7.46	0.1837	152	0.1792	3230	X-RAY DIFFRACTION	100
7.46-124.61	0.2276	196	0.1875	3360	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.9424	-0.2691	0.1942	2.3498	-0.0347	2.0815	0.0473	0.0649	0.2235	-0.3489	0.0588	-0.2812	-0.1871	0.2046	-0.0958	0.4807	-0.0531	0.1029	0.3803	0.0507	0.3803	-48.4982	34.2079	-55.8537
2	0.7933	-0.1842	-0.1169	1.1607	0.0152	1.3234	-0.0359	-0.1319	-0.0673	0.122	0.0928	0.0918	0.0342	-0.1252	-0.0544	0.3027	0.0154	0.0058	0.3165	0.0391	0.3424	-58.3991	11.4751	-29.9849
3	0.6357	-0.2695	0.0779	1.6058	-0.4603	1.4818	-0.0131	-0.0147	0.0482	-0.1244	0.1652	0.1483	-0.2175	-0.1909	-0.1472	0.3088	0.0159	0.0035	0.3097	0.0325	0.3134	-62.0684	27.1987	-43.1301
4	1.7915	-0.7601	0.9137	1.8794	-1.0106	1.0279	-0.0272	0.1939	0.1291	-0.3408	0.1313	0.2112	0.0271	-0.0624	-0.1051	0.4825	-0.0335	-0.0727	0.457	0.0361	0.4105	-69.0572	25.2631	-64.3552
5	3.8749	0.5569	-0.2489	2.8586	0.1693	4.6327	-0.0464	0.5098	-0.4931	-0.2956	0.016	0.6231	0.7822	-0.499	-0.0199	0.7249	-0.1116	-0.1787	0.5162	0.0514	0.6699	-79.2302	21.2706	-64.6856
6	2.0773	-0.1937	1.4923	1.565	0.5397	3.68	-0.1951	-0.0507	0.3004	0.2382	0.0773	-0.2447	-0.1991	0.3748	0.1077	0.3682	-0.0011	-0.0014	0.426	-0.0013	0.4118	-22.1372	15.7351	-6.4617
7	0.8938	-0.2869	-0.0227	1.078	-0.274	1.0926	-0.1274	-0.1688	-0.1828	0.1304	0.1593	0.0591	0.1221	-0.0119	-0.0324	0.3959	0.0805	0.023	0.4257	0.0579	0.3683	-38.2461	-8.8971	-8.2615
8	0.6695	0.0693	0.3846	1.3073	0.18	1.1871	-0.1575	-0.2134	-0.0726	0.2722	0.1283	-0.028	0.0648	0.0631	0.0252	0.3928	0.1266	0.0357	0.4325	0.0426	0.3058	-32.3337	-6.0173	-3.5081
9	2.0872	0.2239	-0.3743	1.7364	0.4897	1.786	-0.2341	-0.6949	-0.048	0.5766	0.0926	-0.0793	0.1416	-0.0471	0.1456	0.654	0.1602	-0.0548	0.737	0.008	0.4604	-23.068	1.7235	16.7445
10	2.7279	0.3463	0.602	1.2229	0.1422	1.9671	-0.0745	-0.2585	0.3082	0.1972	0.1532	-0.0038	-0.3807	0.0549	-0.0891	0.5082	0.1318	-0.0087	0.4885	-0.04	0.3855	-36.3299	17.3788	2.5615
11	0.039	-0.2027	0.0092	1.4249	0.4612	2.0251	-0.1043	-0.4415	0.2754	0.3467	0.0673	0.1715	-0.3154	-0.6291	0.0507	0.5669	0.2049	0.0549	0.6296	-0.0206	0.4496	-47.7263	19.5423	6.8693
12	2.7416	-0.9513	0.9992	3.9086	-0.2044	4.8137	-0.1086	0.0625	-0.0536	0.116	0.2669	-0.9155	-0.1285	0.7918	-0.1281	0.3735	-0.018	0.0268	0.6598	-0.1448	0.7344	-5.3407	-17.2854	-51.1378
13	3.0284	-2.1686	-1.3132	3.0333	1.5864	2.2006	0.0848	-0.1541	0.3182	0.0611	0.2067	-0.5659	0.0425	0.37	-0.2991	0.4225	-0.0535	-0.0162	0.4238	-0.0712	0.5492	-15.4965	-7.7682	-38.4203
14	0.6844	-0.2216	-0.0726	0.7604	0.2891	0.8181	-0.0671	-0.0079	-0.1559	0.0367	0.1158	-0.0564	0.1703	0.0457	-0.0527	0.3605	-0.0141	0.0146	0.2716	-0.0281	0.3809	-31.4962	-22.7295	-46.144
15	1.3536	0.6692	0.2855	2.014	0.7112	2.9613	0.1482	-0.759	0.178	1.1962	-0.1307	0.1543	0.2172	0.0948	-0.0204	1.3249	-0.0614	0.0887	0.9736	-0.1009	0.6036	-31.1	-55.7485	-30.2012

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 278 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 279 through 462 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 463 through 629 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 630 through 677 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 24 through 84 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 85 through 245 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 246 through 382 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 383 through 432 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 433 through 507 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 508 through 562 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 3 through 47 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 48 through 84 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 85 through 551 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 552 through 677 )

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Yorodumi