7F9C: Homo sapiens Prolyl-tRNA Synthetase

Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96. Determined by X-ray diffraction at 2.2 Å resolution. Released 6 Jul 2022.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,986
Mol. weight: 116.8 kDa
Ligands: 1UI, ZN, CA, PRO
Released: 6 Jul 2022

Explore 7F9C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7F9C contains 48 α-helices and 66 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: 24 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	1081-1082	2	4
α-helix	1084-1087	4
α-helix	1091-1097	7
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	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
α-helix	1216	1
β-strand	1221-1229	9	2
β-strand	1234-1245	12	2
α-helix	1249-1252	4
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	1317-1335	19
β-strand	1341-1343	3	8
α-helix	1351-1361	11
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
α-helix	1488-1490	3
α-helix	1493	1
β-strand	1494	1	10
α-helix	1495	1
β-strand	1501	1	10
β-strand	1504-1509	6	9
β-strand	1510-1511	2	2

Chain B: 24 helices, 34 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	1081-1082	2	4
α-helix	1084-1088	5
α-helix	1091-1097	7
α-helix	1098-1100	3
β-strand	1102-1107	6	4
β-strand	1110-1118	9	4
α-helix	1123-1133	11
β-strand	1136	1	12
α-helix	1137-1139	3
β-strand	1142-1151	10	11
α-helix	1157-1158	2
β-strand	1159	1	13
β-strand	1163	1	13
β-strand	1166-1176	11	11
α-helix	1179-1195	17
α-helix	1196-1200	5
β-strand	1206-1209	4	11
α-helix	1216	1
β-strand	1221-1229	9	11
β-strand	1234-1245	12	11
α-helix	1247-1252	6
β-strand	1255-1256	2	14
β-strand	1257	1	12
β-strand	1266-1267	2	14
α-helix	1268	1
β-strand	1269-1276	8	11
α-helix	1278-1287	10
β-strand	1289	1	15
β-strand	1292	1	15
β-strand	1304-1308	5	16
α-helix	1318-1336	19
β-strand	1341-1343	3	16
α-helix	1351-1360	10
β-strand	1365-1369	5	16
α-helix	1371-1375	5
β-strand	1378-1383	6	16
β-strand	1389-1393	5	16
α-helix	1394-1396	3
α-helix	1397-1423	27
β-strand	1424-1426	3	17
α-helix	1430-1438	9
β-strand	1442-1447	6	17
α-helix	1451-1463	13
β-strand	1477-1480	4	17
β-strand	1481-1482	2	11
α-helix	1489-1490	2
α-helix	1493	1
β-strand	1494	1	18
α-helix	1495	1
β-strand	1501	1	18
β-strand	1504-1509	6	17
β-strand	1511	1	11

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

>7F9C_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
1UI	4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-…	C28 H26 F N5 O3	2
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	6
PRO	Proline	C5 H9 N O2	2

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

Primary citation

Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. Yogavel, M., Bougdour, A., Mishra, S. et al. PLoS Pathog (2023) 19:e1011124-e1011124. DOI 10.1371/journal.ppat.1011124 · 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
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

Browse structure collections

About this viewer

MolViewer shows 7F9C directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.