Structure of PDB 2zxf Chain A Binding Site BS01

Receptor Information
>2zxf 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 IDB4P
InChIInChI=1S/C20H28N10O19P4/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(45-19)1-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-2-8-12(32)14(34)20(46-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyYOAHKNVSNCMZGQ-XPWFQUROSA-N
SMILES
SoftwareSMILES
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)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)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[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
FormulaC20 H28 N10 O19 P4
NameBIS(ADENOSINE)-5'-TETRAPHOSPHATE
ChEMBLCHEMBL339385
DrugBank
ZINCZINC000096014967
PDB chain2zxf Chain A Residue 1101 [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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PDB2zxf Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis
Resolution3.4 Å
Binding residue
(original residue number in PDB)		F144 D146 D193 R277 E279 I287 R288 V289 F292 M294 N381 E403 R529
Binding residue
(residue number reindexed from 1)		F81 D83 D130 R214 E216 I224 R225 V226 F229 M231 N318 E340 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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2zxf, PDBe:2zxf, PDBj:2zxf
PDBsum2zxf
PubMed
UniProtP41250|GARS_HUMAN Glycine--tRNA ligase (Gene Name=GARS1)

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