7Y28: Bifunctional glutamate/proline--tRNA ligase

Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1. Determined by X-ray diffraction at 2.29 Å resolution. Released 5 Jul 2023.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,880
Mol. weight: 115.21 kDa
Ligands: F96, ZN, MG, ATP
Released: 5 Jul 2023

Explore 7Y28 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y28 contains 41 α-helices and 62 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	1024-1034	11
β-strand	1038-1040	3	1
β-strand	1047-1049	3	1
α-helix	1051-1070	20
β-strand	1074-1075	2	2
β-strand	1077	1	3
β-strand	1081-1083	3	4
α-helix	1084-1089	6
α-helix	1095-1100	6
β-strand	1102-1107	6	4
β-strand	1110-1118	9	4
α-helix	1123-1133	11
α-helix	1137-1139	3
β-strand	1142-1151	10	2
α-helix	1157-1158	2
β-strand	1159	1	5
β-strand	1163	1	5
β-strand	1166-1176	11	2
α-helix	1179-1195	17
α-helix	1196-1200	5
β-strand	1206-1209	4	2
β-strand	1221-1229	9	2
α-helix	1230-1232	3
β-strand	1234-1245	12	2
α-helix	1247-1252	6
β-strand	1255-1257	3	6
β-strand	1265-1267	3	6
α-helix	1268	1
β-strand	1269-1276	8	2
α-helix	1278-1287	10
β-strand	1289	1	7
β-strand	1292	1	7
β-strand	1304-1308	5	8
α-helix	1317-1336	20
β-strand	1341-1343	3	8
α-helix	1351-1360	10
β-strand	1365-1369	5	8
α-helix	1371-1375	5
β-strand	1378-1383	6	8
β-strand	1389-1393	5	8
α-helix	1394-1396	3
α-helix	1397-1423	27
β-strand	1424-1426	3	9
α-helix	1430-1438	9
β-strand	1442-1447	6	9
α-helix	1451-1460	10
β-strand	1477-1480	4	9
β-strand	1481-1482	2	2
β-strand	1494	1	10
β-strand	1501	1	10
β-strand	1504-1509	6	9
β-strand	1511	1	2

Chain B: 21 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	1024-1034	11
β-strand	1038-1040	3	3
β-strand	1047-1049	3	3
α-helix	1051-1070	20
β-strand	1074-1075	2	11
β-strand	1077	1	1
β-strand	1081-1083	3	4
α-helix	1084-1088	5
α-helix	1098-1100	3
β-strand	1102-1107	6	4
β-strand	1110-1118	9	4
α-helix	1123-1133	11
α-helix	1137-1139	3
β-strand	1142-1151	10	11
α-helix	1157-1158	2
β-strand	1159	1	12
β-strand	1163	1	12
β-strand	1166-1176	11	11
α-helix	1179-1195	17
α-helix	1196-1200	5
β-strand	1206-1209	4	11
β-strand	1221-1229	9	11
α-helix	1230-1232	3
β-strand	1234-1245	12	11
α-helix	1247-1252	6
β-strand	1255-1257	3	13
β-strand	1265-1267	3	13
α-helix	1268	1
β-strand	1269-1276	8	11
α-helix	1278-1287	10
β-strand	1289	1	14
β-strand	1292	1	14
β-strand	1304-1308	5	15
α-helix	1321-1335	15
β-strand	1341-1343	3	15
α-helix	1351-1361	11
β-strand	1365-1369	5	15
α-helix	1371-1375	5
β-strand	1378-1383	6	15
β-strand	1389-1393	5	15
α-helix	1394-1396	3
α-helix	1397-1423	27
β-strand	1424-1426	3	16
α-helix	1430-1437	8
β-strand	1442-1447	6	16
α-helix	1451-1460	10
α-helix	1476	1
β-strand	1477-1480	4	16
β-strand	1481-1482	2	11
β-strand	1504-1509	6	16
β-strand	1511	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional glutamate/proline--tRNA ligase	A, B	protein	497	Homo sapiens	P07814 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7Y28_1 Bifunctional glutamate/proline--tRNA ligase (chains A, B)
LEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFDAEIKKLGVEN
CYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQ
SHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVLQILDLYAQ
VYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIV
FEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGITNAL
SEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEVGPRDMK
SCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASEDLKTHMVVANTMEDFQK
ILDSGKIVQIPFCGEIDCEDWIKKTTARDQDLEPGAPSMGAKSLCIPFKPLCELQPGAKC
VCGKNPAKYYTLFGRSY

Ligands and cofactors

ID	Name	Formula	Copies
F96	1-[6-(3-fluorophenyl)benzimidazol-1-yl]-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]pro…	C21 H22 F N3 O2	2
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	4
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1. Yoon, I., Kim, S., Cho, M. et al. EMBO Mol Med (2023) 15:e16940-e16940. DOI 10.15252/emmm.202216940 · PubMed

Other PDB entries of the same protein (UniProt P07814 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7X09 1.7 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with inhibitors L95 and…
7F99 1.98 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
7Y1H 1.99 Å, Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1
7F9B 2.0 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
7F98 2.0 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
7F9A 2.0 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L97
4HVC 2.0 Å, Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP…
7X1O 2.04 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with double inhibitors HF and L95
5A1N 2.1 Å, The crystal structure of the GST-like domains complex of EPRS-AIMP2 mutant S156D
7BBU 2.19 Å, Crystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline
7F9C 2.2 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
7OSY 2.23 Å, Human Prolyl-tRNA Synthetase in Complex with L-proline

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