PDB-8ytk: Crystal structure of human prolyl-tRNA synthetase in complex with...

ID or keywords:

Entry

Database: PDB / ID: 8ytk

Title

Crystal structure of human prolyl-tRNA synthetase in complex with inhibitor

Components

Bifunctional glutamate/proline--tRNA ligase

Keywords

LIGASE / Prolyl-tRNA synthetase / Inhibitor / Complex

Function / homology

Function and homology information

regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / Selenoamino acid metabolism / glutamate-tRNA ligase activity / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.553 Å

Authors

Luo, Z. / Zhou, H.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Development of Potent Inhibitors Against Bacterial Prolyl-tRNA Synthetase Using Fluorine Scanning
Authors: Luo, Z. / Qiu, H. / Tan, Q. / Chen, B. / Xu, J. / Gu, Q. / Zhou, H.

History

Deposition	Mar 26, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ytk.cif.gz	496.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8ytk.ent.gz	312.3 KB	Display	PDB format
PDBx/mmJSON format	8ytk.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/yt/8ytk ftp://data.pdbj.org/pub/pdb/validation_reports/yt/8ytk	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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (15) #212 - Aug 2017 Glutathione Transferases similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Bifunctional glutamate/proline--tRNA ligase

B: Bifunctional glutamate/proline--tRNA ligase

hetero molecules

120 kDa, 2 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)	71.602, 92.157, 86.621
Angle α, β, γ (deg.)	90.000, 108.629, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Bifunctional glutamate/proline--tRNA ligase / Bifunctional aminoacyl-tRNA synthetase / Cell proliferation-inducing gene 32 protein / Glutamatyl- ...Bifunctional aminoacyl-tRNA synthetase / Cell proliferation-inducing gene 32 protein / Glutamatyl-prolyl-tRNA synthetase Mass: 59594.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli) References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase
#2: Chemical	ChemComp-W2H / (2~{S})-~{N}-[3-(4-azanylquinazolin-7-yl)phenyl]sulfonylpyrrolidine-2-carboxamide Mass: 397.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₁₉N₅O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H₂O
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: 2.28 Å³/Da / Density % sol: 45.97 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.4, 20% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.55→50 Å / Num. obs: 34745 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC_1/2: 0.975 / R_merge(I) obs: 0.195 / Net I/σ(I): 26.4
Reflection shell	Resolution: 2.55→2.59 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.119 / Mean I/σ(I) obs: 7.85 / Num. unique obs: 1713 / CC_1/2: 0.975 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.553→46.121 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.905 / WR_factor R_free: 0.266 / WR_factor R_work: 0.214 / SU B: 21.641 / SU ML: 0.233 / Average fsc free: 0.9565 / Average fsc work: 0.9722 / Cross valid method: FREE R-VALUE / ESU R: 0.883 / ESU R Free: 0.311
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2496	1797	5.193 %
R_work	0.2023	32810	-
all	0.205	-	-
obs	-	34607	99.46 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 44.659 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.265 Å²	0 Å²	-0.9 Å²
2-	-	3.652 Å²	-0 Å²
3-	-	-	-1.451 Å²

Refinement step

Cycle: LAST / Resolution: 2.553→46.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7362	0	68	102	7532

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	7612
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6971
X-RAY DIFFRACTION	r_angle_refined_deg	1.067	1.812	10358
X-RAY DIFFRACTION	r_angle_other_deg	0.41	1.748	15992
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.82	5	950
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.855	5	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.784	10	1130
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.673	10	316
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1152
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9168
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1744
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	1455
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	6524
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	3698
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	3864
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	203
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.099	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.104	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	54
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.058	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.503	2.525	3824
X-RAY DIFFRACTION	r_mcbond_other	0.503	2.525	3824
X-RAY DIFFRACTION	r_mcangle_it	0.862	4.536	4766
X-RAY DIFFRACTION	r_mcangle_other	0.862	4.536	4767
X-RAY DIFFRACTION	r_scbond_it	0.56	2.562	3788
X-RAY DIFFRACTION	r_scbond_other	0.56	2.563	3789
X-RAY DIFFRACTION	r_scangle_it	0.942	4.698	5592
X-RAY DIFFRACTION	r_scangle_other	0.942	4.699	5593
X-RAY DIFFRACTION	r_lrange_it	2.234	30.324	31609
X-RAY DIFFRACTION	r_lrange_other	2.234	30.324	31609

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.553-2.619	0.323	121	0.249	2354	0.253	2545	0.939	0.967	97.2495	0.221
2.619-2.691	0.292	122	0.254	2355	0.256	2479	0.95	0.959	99.9193	0.224
2.691-2.768	0.289	138	0.246	2282	0.249	2422	0.949	0.967	99.9174	0.218
2.768-2.853	0.293	134	0.232	2205	0.236	2341	0.945	0.968	99.9146	0.212
2.853-2.946	0.306	125	0.235	2148	0.238	2280	0.945	0.967	99.693	0.215
2.946-3.049	0.302	123	0.237	2098	0.241	2225	0.941	0.965	99.8202	0.224
3.049-3.164	0.279	114	0.228	2004	0.231	2130	0.956	0.968	99.4366	0.218
3.164-3.293	0.24	97	0.207	1953	0.209	2057	0.962	0.974	99.6597	0.202
3.293-3.438	0.264	113	0.2	1861	0.203	1976	0.959	0.976	99.8988	0.198
3.438-3.605	0.213	86	0.193	1784	0.194	1872	0.97	0.978	99.8932	0.195
3.605-3.799	0.21	94	0.19	1691	0.191	1788	0.976	0.981	99.8322	0.195
3.799-4.027	0.265	81	0.179	1633	0.183	1718	0.962	0.981	99.7672	0.187
4.027-4.303	0.225	85	0.162	1492	0.166	1585	0.97	0.984	99.4953	0.178
4.303-4.645	0.202	81	0.152	1409	0.155	1496	0.975	0.985	99.5989	0.177
4.645-5.083	0.172	65	0.154	1317	0.155	1391	0.981	0.985	99.353	0.18
5.083-5.674	0.216	53	0.188	1176	0.19	1233	0.972	0.98	99.6756	0.221
5.674-6.535	0.219	48	0.219	1065	0.219	1119	0.969	0.972	99.4638	0.256
6.535-7.964	0.26	56	0.225	884	0.227	947	0.971	0.97	99.2608	0.265
7.964-11.099	0.22	39	0.187	688	0.189	732	0.974	0.979	99.3169	0.245
11.099-46.121	0.491	22	0.351	410	0.358	449	0.851	0.932	96.2138	0.56

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	2.1301	1.1005	-0.8796	2.7456	0.2065	3.5593	-0.184	0.4436	0.4122	-0.4683	0.1785	0.1794	-0.6961	-0.3433	0.0055	0.2249	0.0006	-0.0674	0.1162	0.0455	0.1578	2.598	-12.039	3.292
2	1.7904	0.2059	0.2775	1.2665	-0.0314	2.431	-0.1051	0.0691	0.0392	-0.0121	-0.0203	-0.1797	-0.1059	0.2633	0.1254	0.0386	-0.0171	0.0288	0.033	0.025	0.1278	24.149	-17.578	19.28
3	2.8812	3.19	1.629	3.7085	1.6241	1.3513	-0.1493	0.1162	0.1127	-0.3233	0.1029	0.217	0.0013	0.0733	0.0464	0.2827	-0.038	-0.0173	0.1135	-0.0365	0.1635	-0.356	-30.762	-8.185
4	1.4231	0.0663	0.0093	3.3072	0.063	3.5765	-0.1847	0.6092	0.3804	-0.3139	0.119	-0.2731	-0.4801	0.2486	0.0656	0.2849	-0.1504	0.1003	0.3096	0.1564	0.2767	31.144	-2.576	-2.537
5	2.9546	-0.5741	1.7074	1.8747	-1.1142	2.865	-0.0417	-0.2505	0.0601	0.3183	-0.0579	0.0774	0.114	-0.279	0.0996	0.1198	-0.0438	0.0688	0.0502	-0.0135	0.095	6.603	-26.645	30.097
6	1.981	0.1885	0.1073	1.7535	-0.2513	1.873	0.0276	-0.267	0.0457	0.1203	-0.0792	0.3087	0.0514	-0.5657	0.0516	0.055	-0.0376	0.0858	0.2109	-0.0579	0.1437	-6.766	-23.432	25.76
7	5.3389	-0.9188	0.0723	2.825	0.1075	1.2964	0.2465	0.3719	-0.7434	-0.1937	-0.1874	-0.1816	0.5873	0.2349	-0.0591	0.4866	0.069	-0.0144	0.1333	0.0328	0.3192	20.712	-51.07	29.418
8	1.9548	-0.6219	0.3092	3.4206	1.6202	4.2152	-0.2999	-1.0263	-0.234	0.6028	0.2183	0.401	0.2524	-1.0457	0.0815	0.4992	-0.0698	0.1396	0.8627	0.1058	0.3291	-11.901	-36.279	49.948
9	4.4809	-2.1453	0.4409	1.6358	0.3251	4.1701	-0.1186	-0.9307	-0.1436	0.1296	0.3409	0.3443	0.2531	-0.9937	-0.2223	0.3202	-0.1426	0.177	0.8337	0.1182	0.2995	-16.78	-34.84	44.497

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1016 - 1056
2	X-RAY DIFFRACTION	2	ALL	A	1057 - 1277
3	X-RAY DIFFRACTION	3	ALL	A	1278 - 1414
4	X-RAY DIFFRACTION	4	ALL	A	1415 - 1512

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