7X09: Homo sapiens Prolyl-tRNA Synthetase

Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with inhibitors L95 and Halofuginone. Determined by X-ray diffraction at 1.7 Å resolution. Released 30 Aug 2023.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,196
Mol. weight: 117.34 kDa
Ligands: CA, ZN, JE6, HFG
Released: 30 Aug 2023

Explore 7X09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7X09 contains 43 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, 30 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	1084-1087	4
β-strand	1102-1107	6	4
β-strand	1110-1118	9	4
α-helix	1119	1
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
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
α-helix	1474-1476	3
β-strand	1477-1480	4	9
β-strand	1481-1482	2	2
β-strand	1504-1509	6	9
β-strand	1511	1	2

Chain B: 23 helices, 32 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	10
β-strand	1077	1	1
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	1119	1
α-helix	1123-1133	11
α-helix	1137-1139	3
β-strand	1142-1151	10	10
α-helix	1157-1158	2
β-strand	1159	1	11
β-strand	1163	1	11
β-strand	1166-1176	11	10
α-helix	1179-1195	17
α-helix	1196-1200	5
β-strand	1206-1209	4	10
β-strand	1221-1229	9	10
β-strand	1234-1245	12	10
α-helix	1247-1252	6
β-strand	1255-1256	2	12
β-strand	1266-1267	2	12
α-helix	1268	1
β-strand	1269-1276	8	10
α-helix	1278-1287	10
β-strand	1289	1	13
β-strand	1292	1	13
β-strand	1304-1308	5	14
α-helix	1319-1336	18
β-strand	1341-1343	3	14
α-helix	1351-1360	10
β-strand	1365-1369	5	14
α-helix	1371-1375	5
β-strand	1378-1383	6	14
β-strand	1389-1393	5	14
α-helix	1394-1396	3
α-helix	1397-1423	27
β-strand	1424-1426	3	15
α-helix	1430-1438	9
β-strand	1442-1447	6	15
α-helix	1451-1464	14
β-strand	1477-1480	4	15
β-strand	1481-1482	2	10
α-helix	1488-1490	3
α-helix	1493	1
β-strand	1494	1	16
α-helix	1495	1
β-strand	1501	1	16
β-strand	1504-1509	6	15
β-strand	1511	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional glutamate/proline--tRNA ligase	A, B	protein	505	Homo sapiens	P07814 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7X09_1 Bifunctional glutamate/proline--tRNA ligase (chains A, B)
PKKQTRLGLEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFDAE
IKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPIAIRPTSETVMY
PAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVL
QILDLYAQVYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAIQGGTSHHLGQN
FSKMFEIVFEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVII
PCGITNALSEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRL
EVGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASEDLKTHMVVA
NTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARDQDLEPGAPSMGAKSLCIPFKPLC
ELQPGAKCVCGKNPAKYYTLFGRSY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3
ZN	Zinc ion	Zn	4
JE6	~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methy…	C22 H22 N4 O2	2
HFG	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-…	C16 H17 Br Cl N3 O3	2

Water and common crystallization additives (CL, GOL, BR) are not listed.

Primary citation

Crystal structure of Homo sapiens Prolyl-tRNA synthetase (HsPRS) with double inhibitors (HF and L95). Manickam, Y., Babbar, P., Sharma, A. To be published.

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

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
7Y28 2.29 Å, Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1

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