5VAD: Human Prolyl-tRNA synthetase

Crystal structure of human Prolyl-tRNA synthetase (PRS) in complex with inhibitor. Determined by X-ray diffraction at 2.36 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 2.36 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,849
Mol. weight: 117.9 kDa
Ligands: 91Y, ZN, PRO
Released: 31 May 2017

Explore 5VAD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VAD contains 45 α-helices and 60 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: 23 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	1081-1082	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	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
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
α-helix	1297-1299	3
β-strand	1304-1308	5	8
α-helix	1317-1335	19
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	2
α-helix	1430-1438	9
β-strand	1442-1447	6	2
α-helix	1451-1459	9
β-strand	1476-1482	7	2
β-strand	1494	1	9
β-strand	1501	1	9
β-strand	1504-1511	8	2

Chain B: 22 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	10
β-strand	1077	1	1
β-strand	1081-1083	3	4
α-helix	1084-1087	4
α-helix	1093-1097	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	10
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	1247-1251	5
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	1304-1308	5	13
α-helix	1317-1336	20
β-strand	1341-1343	3	13
α-helix	1351-1360	10
β-strand	1365-1369	5	13
α-helix	1371-1375	5
β-strand	1378-1383	6	13
β-strand	1389-1393	5	13
α-helix	1394-1396	3
α-helix	1397-1423	27
β-strand	1424-1426	3	14
α-helix	1430-1437	8
β-strand	1442-1447	6	14
α-helix	1451-1461	11
β-strand	1477-1480	4	14
β-strand	1481-1482	2	10
α-helix	1488-1490	3
α-helix	1493	1
β-strand	1494	1	15
α-helix	1495	1
β-strand	1501	1	15
β-strand	1504-1509	6	14
β-strand	1511	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional glutamate/proline--tRNA ligase	A, B	protein	516	Homo sapiens	P07814 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VAD_1 Bifunctional glutamate/proline--tRNA ligase (chains A, B)
GSSSGAGEGQGPKKQTRLGLEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAI
WEAIKDFFDAEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPI
AIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAF
ATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAI
QGGTSHHLGQNFSKMFEIVFEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLP
PRVACVQVVIIPCGITNALSEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFN
HWELKGVPIRLEVGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRA
SEDLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARDQDLEPGAPSMGA
KSLCIPFKPLCELQPGAKCVCGKNPAKYYTLFGRSY

Ligands and cofactors

ID	Name	Formula	Copies
91Y	3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxam…	C21 H24 N4 O2	2
ZN	Zinc ion	Zn	2
PRO	Proline	C5 H9 N O2	2

Primary citation

Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline. Adachi, R., Okada, K., Skene, R. et al. Biochem Biophys Res Commun (2017) 488:393-399. DOI 10.1016/j.bbrc.2017.05.064 · 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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