Structure of PDB 1b76 Chain B Binding Site BS01

Receptor Information
>1b76 Chain B (length=442) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AASSLDELVALCKRRGFIFQSSEIYGGLQGVYDYGPLGVELKNNLKQAWW
RRNVYERDDMEGLDASVLTHRLVLHYSGHEATFADPMVDNAKARYWTPPR
YFNMMFQDLRGPRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIA
QIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEERLKW
WQEMGLSRENLVPYQQPPESSAHYAKATVDILYRFPHGSLELEGIAQRTD
FDLGSHTKDQEALGITARVLRNEHSTQRLAYRDPETGKWFVPYVIEPSAG
VDRGVLALLAEAFTREELPNGEERIVLKLKPQLAPIKVAVIPLVKNRPEI
TEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTI
GQSKDGTTRLKDTVTVRDRDTMEQIRLHVDELEGFLRERLRW
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 chain1b76 Chain B Residue 2552 [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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PDB1b76 Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R220 F230 R231 V232 F235 Q237 E304 L305 S361 G363 R366
Binding residue
(residue number reindexed from 1)		R157 F167 R168 V169 F172 Q174 E241 L242 S298 G300 R303
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.14: glycine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:1b76, PDBe:1b76, PDBj:1b76
PDBsum1b76
PubMed10064708
UniProtP56206|SYG_THET8 Glycine--tRNA ligase (Gene Name=glyQS)

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