Structure of PDB 5e6m Chain B

Receptor sequence

>5e6mB (length=506) Species: 9606 (Homo sapiens) [Search protein sequence]

IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQ
HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGGQQELADL
FVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLN
FKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDP
SEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLG
YFIGRIYLYLTKVGISPDKLRFRQHMENEMYACDCWDAESKTSYGWIEIV
GCADRSCYDLSCHARATKVPLVAEKPLKEPKTKRFQKTLYVEEVVPNVIE
PSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQE
FMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDT
VNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLF
EGQETG

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

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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	B	D72 R76 Q82 G88 G89 S91 H140 F144 L226 P244 E245 R277 I280 S281 R283 R288 Q547 R548 L567 S568 N570 S599 G601 R602 Y604 A605 R606 T617 D619 F620 T631 R633 Q640 Q675	D9 R13 Q19 G25 G26 S28 H77 F81 L123 P141 E142 R174 I177 S178 R180 R185 Q375 R376 L395 S396 N398 S427 G429 R430 Y432 A433 R434 T445 D447 F448 T459 R461 Q468 Q503
BS02	rna	B	P234 K255 R256 E259 Q262 K264 E429 Y512 V513	P131 K152 R153 E156 Q159 K161 E324 Y340 V341
BS03	GAP	B	R277 I287 V289 F292 E296 E403 I404 E522 S524 G526 R529	R174 I184 V186 F189 E193 E298 I299 E350 S352 G354 R357

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)

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