Structure of PDB 5e6m Chain B Binding Site BS03

Receptor Information
>5e6m Chain B (length=506) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQ
HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGGQQELADL
FVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLN
FKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDP
SEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLG
YFIGRIYLYLTKVGISPDKLRFRQHMENEMYACDCWDAESKTSYGWIEIV
GCADRSCYDLSCHARATKVPLVAEKPLKEPKTKRFQKTLYVEEVVPNVIE
PSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQE
FMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDT
VNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLF
EGQETG
Ligand information
Ligand IDGAP
InChIInChI=1S/C12H17N6O8P/c13-1-6(19)26-27(22,23)24-2-5-8(20)9(21)12(25-5)18-4-17-7-10(14)15-3-16-11(7)18/h3-5,8-9,12,20-21H,1-2,13H2,(H,22,23)(H2,14,15,16)/t5-,8-,9-,12-/m1/s1
InChIKeyHROXHMRQKGGIFT-JJNLEZRASA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P]([O-])(=O)OC(=O)C[NH3+])[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)([O-])OC(=O)C[NH3+])O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P]([O-])(=O)OC(=O)C[NH3+])[C@@H](O)[C@H]3O
ACDLabs 10.04[O-]P(=O)(OC(=O)C[NH3+])OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)([O-])OC(=O)C[NH3+])O)O)N
FormulaC12 H17 N6 O8 P
NameGLYCYL-ADENOSINE-5'-PHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain5e6m Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5e6m Crystal Structure of the Wild-Type Human GlyRS Bound with tRNA(Gly) in a Productive Conformation
Resolution2.927 Å
Binding residue
(original residue number in PDB)		R277 I287 V289 F292 E296 E403 I404 E522 S524 G526 R529
Binding residue
(residue number reindexed from 1)		R174 I184 V186 F189 E193 E298 I299 E350 S352 G354 R357
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.7.-
6.1.1.14: glycine--tRNA ligase.
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5e6m, PDBe:5e6m, PDBj:5e6m
PDBsum5e6m
PubMed27261259
UniProtP41250|GARS_HUMAN Glycine--tRNA ligase (Gene Name=GARS1)

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