Structure of PDB 2zt7 Chain A Binding Site BS02

Receptor Information
>2zt7 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 IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain2zt7 Chain A Residue 1200 [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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PDB2zt7 Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis
Resolution2.7 Å
Binding residue
(original residue number in PDB)		R277 I287 R288 V289 F292 E403 I404 R529
Binding residue
(residue number reindexed from 1)		R214 I224 R225 V226 F229 E340 I341 R386
Annotation score5
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:2zt7, PDBe:2zt7, PDBj:2zt7
PDBsum2zt7
PubMed
UniProtP41250|GARS_HUMAN Glycine--tRNA ligase (Gene Name=GARS1)

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