PDB-37as: Crystal structure of an adenylate kinase from Leishmania major (C...

ID or keywords:

Entry

Database: PDB / ID: 37as

Title

Crystal structure of an adenylate kinase from Leishmania major (C2221 form, ADP and AMP bound)

Components

Putative adenylate kinase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / adenylate kinase

Function / homology

Function and homology information

adenylate kinase / AMP kinase activity / ATP binding / cytoplasm
Similarity search - Function

Biological species

Leishmania major strain Friedlin (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To be published
Title: Crystal structure of an adenylate kinase from Leishmania major (C2221 form, ADP and AMP bound)
Authors: Lanyi Lari, N. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 9, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	37as.cif.gz	192.4 KB	Display	PDBx/mmCIF format
PDB format	pdb37as.ent.gz	152.8 KB	Display	PDB format
PDBx/mmJSON format	37as.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/7a/37as ftp://data.pdbj.org/pub/pdb/validation_reports/7a/37as	HTTPS FTP

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Related structure data

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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Putative adenylate kinase

B: Putative adenylate kinase

hetero molecules

51.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	61.500, 64.529, 241.502
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-437- HOH
2	1	B-409- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Putative adenylate kinase Mass: 24694.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major strain Friedlin (eukaryote) Gene: LMJF_36_1360 / Plasmid: LemaA.00628.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4Q1U0, adenylate kinase

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Non-polymers , 5 types, 252 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.29 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus E9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene ...Details: Morpheus E9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol, LemaA.00628.a.B2.PW39538 at 20.6 mg/mL. plate 21073 A2 drop 1, Soak in 5 mM AMP in crystallant, ADP and AMP bound, Puck: PSL-1710, Cryo: direct

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.29 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus E9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene ...

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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: Jun 20, 2026
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: 1.91→48.3 Å / Num. obs: 37882 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.029 / R_rim(I) all: 0.107 / Χ²: 1 / Net I/σ(I): 14.3 / Num. measured all: 508686
Reflection shell	Resolution: 1.91→1.95 Å / % possible obs: 100 % / Redundancy: 14 % / R_merge(I) obs: 1.894 / Num. measured all: 35405 / Num. unique obs: 2521 / CC_1/2: 0.693 / R_pim(I) all: 0.521 / R_rim(I) all: 1.965 / Χ²: 0.99 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(dev_6116: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.91→44.52 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2264	1860	4.92 %
R_work	0.1857	-	-
obs	0.1878	37809	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.91→44.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3349	0	127	245	3721

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3556
X-RAY DIFFRACTION	f_angle_d	0.925	4807
X-RAY DIFFRACTION	f_dihedral_angle_d	17.418	1444
X-RAY DIFFRACTION	f_chiral_restr	0.054	542
X-RAY DIFFRACTION	f_plane_restr	0.008	623

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 (%)
1.91-1.96	0.3445	128	0.301	2740	X-RAY DIFFRACTION	100
1.96-2.02	0.327	144	0.26	2732	X-RAY DIFFRACTION	100
2.02-2.08	0.2679	138	0.241	2706	X-RAY DIFFRACTION	100
2.08-2.16	0.2731	125	0.2306	2751	X-RAY DIFFRACTION	100
2.16-2.25	0.2721	148	0.1992	2740	X-RAY DIFFRACTION	100
2.25-2.35	0.2587	153	0.1901	2738	X-RAY DIFFRACTION	100
2.35-2.47	0.2193	131	0.1955	2758	X-RAY DIFFRACTION	100
2.47-2.63	0.2531	148	0.1933	2746	X-RAY DIFFRACTION	100
2.63-2.83	0.2832	132	0.2147	2751	X-RAY DIFFRACTION	100
2.83-3.11	0.2811	147	0.2084	2762	X-RAY DIFFRACTION	100
3.11-3.56	0.2242	156	0.1872	2780	X-RAY DIFFRACTION	100
3.56-4.49	0.1945	155	0.1475	2823	X-RAY DIFFRACTION	100
4.49-44.52	0.174	155	0.1639	2922	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	7.2401	-3.771	2.7261	5.0817	-1.5559	3.562	-0.3884	-0.3095	0.1335	0.5965	0.1843	0.2514	-0.5391	-0.4306	0.1655	0.3725	0.0526	0.0578	0.3023	-0.0205	0.2776	-1.4218	21.6882	45.4504
2	8.2908	-3.49	6.9643	7.5695	-5.0373	9.8121	0.1013	-0.131	-0.2452	-0.24	0.1067	0.2904	0.6295	-0.5682	-0.2288	0.3055	-0.0293	0.0357	0.3198	-0.0283	0.2376	-4.7529	12.7834	43.4195
3	3.8905	-3.3571	0.4687	4.8143	3.6442	9.239	-0.311	-0.0477	-0.5994	0.2917	0.0288	0.0539	0.4397	0.2278	0.4268	0.2737	-0.0022	-0.002	0.1882	0.0112	0.3078	6.3775	13.8776	31.2916
4	5.5544	-3.487	3.6322	8.8832	-5.8706	9.111	-0.3623	0.285	0.3111	-0.8175	-0.1807	-0.5708	0.0425	0.4527	0.4691	0.369	-0.0669	0.0499	0.3042	-0.0007	0.341	17.7311	13.811	27.1573
5	8.7619	-1.6998	-2.2108	2.2051	-0.0113	0.6553	0.2694	0.6227	0.0751	0.0024	-0.0962	0.0349	0.1115	-0.267	-0.1627	0.3737	-0.0472	0.0254	0.3697	-0.0098	0.2773	9.7699	23.7604	31.1703
6	8.5889	4.2576	2.2346	4.27	0.4603	3.9804	-0.0602	0.4239	0.4434	0.1693	-0.095	0.4361	0.0447	0.0267	0.1265	0.3439	0.0236	0.0866	0.241	-0.0133	0.3134	-1.074	23.0347	35.7936
7	1.3651	0.1349	-0.6426	6.1255	-0.7242	1.8268	-0.0202	-0.0274	-0.0644	0.0229	-0.0281	-0.1153	0.107	0.0916	0.0579	0.2182	-0.0153	-0.0285	0.2833	0.0246	0.2123	6.4715	12.7304	43.943
8	2.593	1.2585	0.1535	5.8096	0.2926	2.7589	0.0792	-0.1203	-0.2872	-0.0752	-0.0299	-0.8295	0.0415	0.4527	-0.076	0.2567	-0.0082	-0.0282	0.3618	0.0442	0.2976	15.8062	13.8701	43.8412
9	1.0312	-0.7081	0.2653	5.8683	-6.5906	7.6912	-0.1208	-0.3646	0.1211	1.0847	0.2719	-0.1613	-0.7953	0.0975	-0.1768	0.5671	0.0269	0.044	0.3832	-0.0664	0.278	2.6432	21.1301	53.612
10	5.204	-5.2629	1.4704	5.7167	-1.6574	6.8787	-0.198	-0.4574	0.3213	0.0593	0.2339	-0.4862	0.194	-0.3177	-0.022	0.3359	-0.0899	0.0476	0.446	-0.0305	0.2765	-6.5348	15.875	53.6516
11	8.0959	-4.6952	0.9065	8.5726	-4.9179	6.5383	0.0754	0.1352	-0.5404	-0.2599	-0.1152	0.2165	0.3756	0.3177	0.0733	0.3154	-0.0465	-0.0214	0.349	-0.0498	0.2171	21.2023	30.533	15.6936
12	2.4985	-2.7801	3.5637	3.5072	-4.8628	8.2877	0.018	0.0785	-0.1053	-0.3267	0.2293	0.3879	0.4889	-0.4259	-0.2225	0.371	-0.0945	0.0374	0.4211	0.033	0.2808	13.0461	26.3507	16.8558
13	4.2657	-3.4985	-3.7492	3.3306	2.2222	7.9315	-0.3283	0.1733	0.0768	0.2991	0.1256	0.8959	0.3869	0.0088	0.2139	0.2162	-0.0161	0.0641	0.2885	0.0545	0.3845	13.6662	37.7416	29.1186
14	5.4218	-1.7657	3.4852	7.1812	-3.6647	8.1112	0.6736	-0.7433	0.9892	0.8127	-0.3636	0.526	-0.7607	0.0076	-0.2384	0.4367	-0.1425	0.1262	0.483	-0.0375	0.5204	13.0609	49.2851	33.0815
15	5.1272	-3.7342	-0.2859	5.8398	2.5808	2.2547	-0.1049	-0.1505	0.0675	0.8692	0.2763	0.2643	0.1699	0.2097	-0.191	0.3967	-0.0632	0.0358	0.3288	-0.0248	0.3167	23.4237	41.5279	29.1858
16	5.6216	4.0866	-2.0774	3.0023	-1.444	1.7897	-0.0267	0.009	-0.4059	0.5358	-0.1954	-0.1333	0.0843	0.0643	0.246	0.3056	-0.0029	0.0159	0.363	-0.0322	0.2042	23.1055	30.6012	24.5477
17	3.6701	-0.2107	0.1237	2.3405	0.5038	1.0417	-0.0013	0.2317	0.0743	-0.2475	0.0991	-0.0247	-0.1362	-0.0549	-0.0831	0.2376	-0.0385	0.0341	0.3086	0.0563	0.2057	21.8905	39.0571	14.849
18	4.8001	2.0873	-2.3675	3.3974	-4.9285	7.7121	0.0798	-0.0812	-0.3417	0.0154	0.0765	0.3486	0.3025	-0.163	-0.2201	0.3634	0.0102	0.002	0.4006	0.0802	0.4378	1.9641	36.4156	20.432
19	6.1669	1.7697	0.2742	7.751	0.926	6.2811	0.0415	0.1206	0.2136	0.2928	0.0948	0.6383	0.1572	-0.6597	-0.148	0.2475	0.0866	-0.0246	0.4006	0.0993	0.3687	-1.5168	39.1311	19.1429
20	7.8305	-3.8904	-0.3848	6.974	0.0936	3.074	0.0335	0.5229	0.4573	-0.4061	0.011	0.1348	-0.3827	0.1411	-0.1451	0.4051	-0.1104	0.0184	0.2909	0.0458	0.3029	19.5454	49.052	13.5897
21	6.0141	-1.4885	5.7038	2.7354	-0.5123	5.8241	0.2245	0.5227	0.2307	-0.3478	-0.1182	0.0066	-0.3216	0.1965	-0.1742	0.4419	-0.0217	0.0246	0.4857	0.022	0.2658	21.2227	34.5255	6.6224
22	4.2114	-5.9935	-0.7205	9.529	1.7215	2.1974	0.3708	0.9889	0.2336	-0.6204	-0.1107	-0.6311	0.0367	0.3813	-0.3702	0.5783	-0.0949	0.0015	0.6067	-0.0289	0.2909	16.3298	24.932	7.0887

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 45 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 59 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 60 through 76 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 77 through 94 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 95 through 149 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 150 through 181 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 182 through 194 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 195 through 210 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 16 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 17 through 30 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 31 through 45 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 46 through 59 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 60 through 76 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 77 through 94 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 95 through 126 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 127 through 139 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 140 through 160 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 161 through 181 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 182 through 194 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 195 through 210 )

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