PDB-8vka: Crystal structure of Plasmodium vivax glycylpeptide N-tetradecano...

ID or keywords:

Entry

Database: PDB / ID: 8vka

Title

Crystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 9c

Components

Glycylpeptide N-tetradecanoyltransferase

Keywords

TRANSFERASE / Enzyme / Inhibitor / Complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Plasmodium vivax Sal-1 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Fenwick, M.K. / Staker, B.L. / Phan, I.Q. / Early, J. / Myler, P.J. / 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)	R01AI155536	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States

Citation

Journal: J.Med.Chem. / Year: 2024
Title: Exploring Subsite Selectivity within Plasmodium vivax N -Myristoyltransferase Using Pyrazole-Derived Inhibitors.
Authors: Rodriguez-Hernandez, D. / Fenwick, M.K. / Zigweid, R. / Sankaran, B. / Myler, P.J. / Sunnerhagen, P. / Kaushansky, A. / Staker, B.L. / Grotli, M.

History

Deposition	Jan 8, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vka.cif.gz	927 KB	Display	PDBx/mmCIF format
PDB format	pdb8vka.ent.gz		Display	PDB format
PDBx/mmJSON format	8vka.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vka_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	8vka_full_validation.pdf.gz	2.8 MB	Display
Data in XML	8vka_validation.xml.gz	56.5 KB	Display
Data in CIF	8vka_validation.cif.gz	82.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/8vka ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vka	HTTPS FTP

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Related structure data

Related structure data	8vkbC 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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Glycylpeptide N-tetradecanoyltransferase

B: Glycylpeptide N-tetradecanoyltransferase

C: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

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

1

A: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

defined by author&software
47.3 kDa, 1 polymers

2

B: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

defined by author&software
46.8 kDa, 1 polymers

3

C: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

defined by author&software
47.5 kDa, 1 polymers

Unit cell

Length a, b, c (Å)	58.340, 119.279, 173.755
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 3 molecules ABC

#1: Protein	Glycylpeptide N-tetradecanoyltransferase Mass: 45100.566 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PVX_085815 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5K1A2

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Non-polymers , 8 types, 988 molecules

#2: Chemical	ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₅H₆₂N₇O₁₇P₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1AB7 / N-[1,5-dimethyl-4-(2-{[(2M)-2'-(piperazin-1-yl)[2,4'-bipyridin]-3-yl]oxy}ethyl)-1H-pyrazole-3-carbonyl]glycine Mass: 479.532 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₄H₂₉N₇O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical	ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₃₀O₈ / Comment: precipitant*YM
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 951 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.23 Å³/Da / Density % sol: 44.94 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, and 20% PEG 8000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00003 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.97→48.43 Å / Num. obs: 81680 / % possible obs: 94.9 % / Redundancy: 4.6 % / B_iso Wilson estimate: 23.65 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.138 / R_pim(I) all: 0.066 / R_rim(I) all: 0.154 / Χ²: 1.02 / Net I/σ(I): 8 / Num. measured all: 375036
Reflection shell	Resolution: 1.97→2.01 Å / % possible obs: 97.4 % / Redundancy: 4.6 % / R_merge(I) obs: 0.988 / Num. measured all: 20997 / Num. unique obs: 4587 / CC_1/2: 0.693 / R_pim(I) all: 0.469 / R_rim(I) all: 1.1 / Χ²: 0.88 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PDB_EXTRACT		data extraction
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.97→44.87 Å / SU ML: 0.212 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.198	4044	4.96 %
R_work	0.1574	77570	-
obs	0.1593	81614	94.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 28.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→44.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9485	0	391	951	10827

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0098	10939
X-RAY DIFFRACTION	f_angle_d	0.819	14911
X-RAY DIFFRACTION	f_chiral_restr	0.058	1560
X-RAY DIFFRACTION	f_plane_restr	0.0065	1872
X-RAY DIFFRACTION	f_dihedral_angle_d	18.777	4135

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 (%)
1.97-1.99	0.3076	144	0.2375	2706	X-RAY DIFFRACTION	97.07
1.99-2.02	0.2447	127	0.2271	2750	X-RAY DIFFRACTION	96.93
2.02-2.04	0.2846	155	0.2147	2689	X-RAY DIFFRACTION	97.23
2.04-2.07	0.2766	143	0.2131	2701	X-RAY DIFFRACTION	96.8
2.07-2.1	0.2755	165	0.2111	2671	X-RAY DIFFRACTION	96.07
2.1-2.13	0.2275	131	0.1995	2722	X-RAY DIFFRACTION	96.74
2.13-2.16	0.2529	150	0.1817	2730	X-RAY DIFFRACTION	96.61
2.16-2.19	0.2291	143	0.1771	2662	X-RAY DIFFRACTION	96.62
2.19-2.23	0.2122	158	0.1829	2717	X-RAY DIFFRACTION	96.35
2.23-2.27	0.2668	133	0.1958	2684	X-RAY DIFFRACTION	96.01
2.27-2.31	0.2487	152	0.1902	2687	X-RAY DIFFRACTION	95.91
2.31-2.35	0.2146	137	0.1669	2720	X-RAY DIFFRACTION	96
2.35-2.4	0.2321	150	0.1708	2688	X-RAY DIFFRACTION	96.4
2.4-2.45	0.2265	141	0.16	2724	X-RAY DIFFRACTION	96.27
2.45-2.51	0.2165	150	0.1638	2702	X-RAY DIFFRACTION	96.32
2.51-2.57	0.2183	133	0.164	2707	X-RAY DIFFRACTION	96.08
2.57-2.64	0.2514	135	0.1602	2751	X-RAY DIFFRACTION	96.1
2.64-2.72	0.2303	120	0.1696	2668	X-RAY DIFFRACTION	95.28
2.72-2.81	0.2101	162	0.161	2700	X-RAY DIFFRACTION	95.3
2.81-2.91	0.2057	142	0.159	2702	X-RAY DIFFRACTION	94.83
2.91-3.03	0.1812	135	0.1573	2671	X-RAY DIFFRACTION	94.86
3.03-3.16	0.2191	149	0.1482	2663	X-RAY DIFFRACTION	93.55
3.16-3.33	0.1655	122	0.1431	2658	X-RAY DIFFRACTION	92.82
3.33-3.54	0.1629	132	0.1357	2589	X-RAY DIFFRACTION	90.76
3.54-3.81	0.1753	125	0.1223	2617	X-RAY DIFFRACTION	90.79
3.81-4.2	0.1456	106	0.1181	2597	X-RAY DIFFRACTION	88.94
4.2-4.8	0.1216	131	0.1092	2538	X-RAY DIFFRACTION	87.57
4.8-6.05	0.1651	139	0.1387	2553	X-RAY DIFFRACTION	87.2
6.05-44.87	0.1848	134	0.1896	2603	X-RAY DIFFRACTION	84.4

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	0.885231531623	0.0555718768343	0.0367715247524	1.20037988752	0.30480516702	0.833770214899	0.0153060948567	0.022975233529	0.00433773191895	-0.0372732812044	0.0166617967205	-0.0909622891795	0.0149736658367	0.0848972612409	-0.0352040765763	0.162324573714	0.00267936002854	0.00126837657633	0.185915825542	0.00171195019357	0.175824519964	41.4057055932	21.8631934436	14.8810082492
2	1.66684609781	0.85153763129	-0.908094200409	1.1389857435	-0.382119897185	0.480869648569	0.0302413858002	-0.290106110707	-0.197116472918	0.0769326107421	-0.0807460438982	-0.0182437442997	0.126871195209	-0.0410827493889	0.0552289338642	0.226365031246	0.00311253587906	0.00565545726367	0.204011370216	0.00197223548669	0.163010102212	13.3891532025	15.6566541129	28.9489468216
3	2.57981307881	-0.0268809249685	1.2921024192	1.849218613	1.46875213057	4.2362870443	-0.188785783141	0.263036052347	0.259964434526	-0.0433918385585	0.0690941516317	-0.0232850629055	-0.180727939872	0.238422768651	0.0983538715089	0.127366198995	-0.0297272591977	0.0207750599225	0.163528661587	0.0379047055348	0.143473776302	20.2950230359	33.8696821204	11.9570618065
4	1.99524186401	-0.604021565721	0.0134581743919	3.31583583385	-0.173845866716	1.20122800253	-0.0126789309031	-0.124299761009	-0.0797438104241	0.0859173644592	0.0342267684774	0.165665145706	-0.0205893181577	-0.09436429089	-0.0242123097667	0.108290318373	-0.0106646214245	0.0022897996414	0.186259682545	0.0112519726448	0.128381655835	14.5666534316	22.0914465713	22.5143122185
5	6.23918359538	-1.33732808583	-1.35048089783	2.37279032619	-2.2540257687	3.76710626886	0.0451598227662	-0.0618220298461	0.0115749664989	0.0654021691733	0.00917128953364	-0.0324001305137	0.0681662237103	-0.00790355303429	-0.0711782404171	0.139895681025	-0.0167917804028	-0.00225937651184	0.120908015272	-0.0402030339645	0.0970940756053	33.9402073597	31.5552396542	26.0127012588
6	3.6810994784	-1.49459576771	-2.01525567283	3.47710134918	3.37265209603	4.90129670777	-0.00538374449163	0.22016907863	-0.261460902878	-0.265661737992	-0.0734396745006	0.174617699689	0.166282501968	-0.00202214199716	0.0697168860671	0.111604430233	-0.0224283390236	-0.0681332387314	0.253628425945	-0.0294384903908	0.202890465508	-7.79212780884	41.7837873453	38.930658191
7	2.32054289352	-0.134653583411	0.0720483739712	0.850984135841	-0.566242083631	1.63877221509	-0.0324687570696	-0.226940463206	0.0372266237286	0.0893888316445	0.0302317269756	-0.00312276798586	-0.0222031401869	-0.0170518062077	0.00522777939521	0.125409486764	-0.00396267218714	0.00577444140871	0.140257993899	-0.0260218977236	0.138779087776	0.13984782878	47.7756388936	57.6837989595
8	2.67298023835	-1.3454303381	0.221833971108	0.989619419795	-0.316406487995	0.349873518392	0.0437081337052	-0.0926027270398	-0.365561928127	0.08455028407	0.0188309781828	0.12799499171	0.199810167684	-0.0457915320613	-0.126517460346	0.241640039152	0.018364312512	0.00185661615719	0.167660253662	-0.0279777676571	0.250450035773	19.0024941018	28.4989204384	53.4438071409
9	2.09071017689	0.881873314983	-0.647008599404	4.14899025234	-1.2147750311	1.41378546072	0.0290037761181	-0.169508114399	-0.139155005344	-0.251824129202	-0.124008889632	-0.492668228315	0.123806578551	0.241818122485	0.105175399967	0.185766433667	-0.035124469762	-0.0383511628597	0.272115157084	-0.00644975618404	0.196529474575	35.9310550809	39.4576817699	52.4438159591
10	1.93054892229	-0.141808278188	0.297168933871	1.54090344146	-0.567048246028	2.03302951025	-0.0236345599192	0.105713703106	-0.00969699598056	-0.0110647699016	0.00791354438615	-0.0734808900337	-0.0169241004855	0.0628696227601	0.0195199990591	0.0935798497543	-0.0106856116502	0.00926102612639	0.178023837802	-0.0223696619863	0.141793182026	23.9650216771	45.8614281597	48.2581897412
11	6.23763216649	-3.3872729337	1.37293629212	2.79749496801	-0.981809931503	0.660170654733	-0.0145964276077	0.0717046177172	-0.0926372908211	-0.00634637247008	0.0295409839701	-0.0150025568112	0.0366699229248	-0.0428010150609	-0.0214608075894	0.130698535892	-0.013226424242	-0.000759060081198	0.161603068311	-0.0551712427271	0.120003222259	9.04874284967	38.6021181653	42.2489417327
12	2.9491213946	2.20662563622	-0.698290718511	6.33647789569	-0.0221442688244	0.562756242705	-0.0263797804668	0.0846011687708	-0.411856328741	-0.098236844558	0.158657926597	-0.323842862608	0.464675627829	-0.00534037528242	-0.0991502990894	0.164099918189	0.0721201277281	0.00146955677031	0.183465511292	0.00464033300251	0.284585402489	26.385563638	58.6720660432	13.0539819353
13	1.55238377443	-0.096605896849	-0.111942037529	1.07045573331	-0.818204998491	1.79422510968	0.00121536332054	0.045007535804	0.0876576853455	-0.0387373977089	-0.0267604938035	-0.00664988269122	-0.0458146648254	0.0134596678872	0.0222230098552	0.144245484222	-0.000926132844579	0.00430777476529	0.155624915723	-0.0229360594962	0.166168351492	18.4699980138	78.4430935022	8.78646439246
14	6.5881542265	-1.17467921751	2.99730833076	0.190325138077	-0.578436251721	1.29297112078	0.122860899747	0.984987429459	-0.218470674896	-0.204203894972	-0.119285401509	0.117132512791	0.119399922205	0.348672786031	-0.0440287588296	0.253174794056	-0.00297183565421	-0.0408852874394	0.327451331679	-0.050367319743	0.275854025325	-1.55611850299	64.8932648603	-6.76385460459
15	2.09725630256	0.00737807107753	0.0148903548032	1.28006864287	-0.199332241311	1.83214773148	-0.0321753824913	0.110569038747	-0.0401760362368	-0.0129547569374	0.0459763709035	0.169257647718	0.0431174816669	-0.148894987854	-0.0180343287366	0.114860201409	0.000773010495746	0.0115908016289	0.146230700954	0.00301885101651	0.165018269257	-7.05239832006	69.7883456697	11.059065449
16	8.20591077036	0.653970372671	4.1263550332	0.813991716807	0.334885307447	2.77302099788	0.0889567085802	0.289736839518	-0.0100108555153	-0.0682085950786	-0.0969018092954	0.0377930818881	0.115892420911	0.0977568692998	-0.00320533910068	0.17216268129	0.0253227579714	0.0242671723649	0.14453056928	-0.0225137559329	0.15659769089	9.91093018479	60.1272542792	8.48265015751

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 27 through 198 )	A	A	27 - 198	1 - 172
2	2	chain 'A' and (resid 199 through 257 )	A	A	199 - 257	173 - 231
3	3	chain 'A' and (resid 258 through 296 )	A	A	258 - 296	232 - 270
4	4	chain 'A' and (resid 297 through 386 )	A	A	297 - 386	271 - 360
5	5	chain 'A' and (resid 387 through 410 )	A	A	387 - 410	361 - 384
6	6	chain 'B' and (resid 26 through 59 )	B	B	26 - 59	1 - 34
7	7	chain 'B' and (resid 60 through 198 )	B	B	60 - 198	35 - 173
8	8	chain 'B' and (resid 199 through 234 )	B	B	199 - 234	174 - 209
9	9	chain 'B' and (resid 235 through 257 )	B	B	235 - 257	210 - 232
10	10	chain 'B' and (resid 258 through 379 )	B	B	258 - 379	233 - 354
11	11	chain 'B' and (resid 380 through 410 )	B	B	380 - 410	355 - 385
12	12	chain 'C' and (resid 26 through 59 )	C	C	26 - 59	1 - 34
13	13	chain 'C' and (resid 60 through 198 )	C	C	60 - 198	35 - 173
14	14	chain 'C' and (resid 199 through 241 )	C	C	199 - 241	174 - 216
15	15	chain 'C' and (resid 242 through 379 )	C	C	242 - 379	217 - 354
16	16	chain 'C' and (resid 380 through 410 )	C	C	380 - 410	355 - 385

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