Structure of PDB 5e6m Chain A

Receptor sequence

>5e6mA (length=519) Species: 9606 (Homo sapiens) [Search protein sequence]

EEVLAPLRLAVRQQGDLVRKLKEDVDKAVAELKARKRVLEAKELALQPKD
DIVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWR
QHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFVSFNLMFKTFIGPGG
NMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGL
IRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKM
RLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMACD
CWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKFQK
TLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAP
FKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDE
IGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGN
ITWADVEARYPLFEGQETG

3D structure

PDB

5e6m Crystal Structure of the Wild-Type Human GlyRS Bound with tRNA(Gly) in a Productive Conformation

Chain

Resolution

2.927 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Enzyme Commision number

2.7.7.-
6.1.1.14: glycine--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)
BS01	rna	A	P234 K255 R256 E259 K264 E429 Y512 V513	P148 K169 R170 E173 K178 E340 Y353 V354
BS02	rna	A	R67 D72 R76 Q82 G88 G89 S91 F144 L226 P244 R277 S281 R283 R288 Q547 R548 L567 S568 N570 S599 G601 R602 Y604 A605 R606 E609 T617 D619 F620 T631 R633 Q640 F672 Q675	R55 D60 R64 Q70 G76 G77 S79 F132 L140 P158 R191 S195 R197 R202 Q388 R389 L408 S409 N411 S440 G442 R443 Y445 A446 R447 E450 T458 D460 F461 T472 R474 Q481 F513 Q516
BS03	GAP	A	E245 R277 R288 V289 F292 E296 E403 I404 E522 S524 G526 R529	E159 R191 R202 V203 F206 E210 E314 I315 E363 S365 G367 R370

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0004081	bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity
GO:0004812	aminoacyl-tRNA ligase activity
GO:0004820	glycine-tRNA ligase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0016740	transferase activity
GO:0016787	hydrolase activity
GO:0042802	identical protein binding
GO:0046983	protein dimerization activity
GO:0141192	ATP:ATP adenylyltransferase activity

	Biological Process
GO:0006412	translation
GO:0006418	tRNA aminoacylation for protein translation
GO:0006426	glycyl-tRNA aminoacylation
GO:0015966	diadenosine tetraphosphate biosynthetic process
GO:0070150	mitochondrial glycyl-tRNA aminoacylation

	Cellular Component
GO:0005576	extracellular region
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005829	cytosol
GO:0030141	secretory granule
GO:0030424	axon
GO:0042995	cell projection
GO:0070062	extracellular exosome

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5e6m, PDBe:5e6m, PDBj:5e6m
PDBsum	5e6m
PubMed	27261259
UniProt	P41250\|GARS_HUMAN Glycine--tRNA ligase (Gene Name=GARS1)

[Back to BioLiP]