Structure of PDB 5vad Chain B

Receptor sequence

>5vadB (length=482) Species: 9606 (Homo sapiens)

LEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFD
AEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEP
IAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTR
EFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEK
FAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGEK
QFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGILSEE
DKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLE
VGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASE
DLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARMGAKS
LCIPFKPLCELQPGAKCVCNPAKYYTLFGRSY

3D structure

• PDB: 5vad Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline.
• Chain: B
• Resolution: 2.36 Å

Enzymatic activity

• Enzyme Commision number: 6.1.1.15: proline--tRNA ligase.
  6.1.1.17: glutamate--tRNA ligase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	91Y	B	R1152 E1154 K1156 F1161 L1162 R1163 T1164 F1167 T1240 T1276 R1278	R137 E139 K141 F146 L147 R148 T149 F152 T225 T261 R263	MOAD: Kd=0.76nM
BS02	PRO	B	T1121 E1123 R1152 W1169 E1171 F1216 H1242 W1273 G1274	T106 E108 R137 W154 E156 F201 H227 W258 G259
BS03	ZN	B	C1453 C1495 C1497	C435 C467 C469

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004827 proline-tRNA ligase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006433 prolyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5vad, PDBe:5vad, PDBj:5vad
• PDBsum: 5vad
• PubMed: 28501621
• UniProt: P07814|SYEP_HUMAN Bifunctional glutamate/proline--tRNA ligase (Gene Name=EPRS1)