Structure of PDB 2zt8 Chain A Binding Site BS01

Receptor Information
>2zt8 Chain A (length=530) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQ
HFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHL
LKAHLQKLMSDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPI
TGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQG
KLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQN
VADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYL
TKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCY
DLSCHARATKVPLVAEKPYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVRE
GDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKV
DDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRA
EISELPSIVQDLANGNITWADVEARYPLFE
Ligand information
Ligand IDDRV
InChIInChI=1S/C12H17N7O7S/c13-1-6(20)18-27(23,24)25-2-5-8(21)9(22)12(26-5)19-4-17-7-10(14)15-3-16-11(7)19/h3-5,8-9,12,21-22H,1-2,13H2,(H,18,20)(H2,14,15,16)/t5-,8-,9+,12+/m0/s1
InChIKeyAMWPZASLDLLQFT-REFFQAGNSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)CN
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)CN)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@@H](O3)COS(=O)(=O)NC(=O)CN)O)O)N
CACTVS 3.341NCC(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341NCC(=O)N[S](=O)(=O)OC[C@@H]1O[C@H]([C@H](O)[C@H]1O)n2cnc3c(N)ncnc23
FormulaC12 H17 N7 O7 S
Name[(2S,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (aminoacetyl)sulfamate
ChEMBL
DrugBank
ZINCZINC000058638464
PDB chain2zt8 Chain A Residue 699 [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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PDB2zt8 Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis
Resolution3.35 Å
Binding residue
(original residue number in PDB)		E245 R277 I287 V289 F292 E296 Y386 E403 I404 V405 E522 G526 R529
Binding residue
(residue number reindexed from 1)		E182 R214 I224 V226 F229 E233 Y323 E340 I341 V342 E379 G383 R386
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2zt8, PDBe:2zt8, PDBj:2zt8
PDBsum2zt8
PubMed
UniProtP41250|GARS_HUMAN Glycine--tRNA ligase (Gene Name=GARS1)

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