Structure of PDB 1ggm Chain B Binding Site BS01

Receptor Information
>1ggm 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 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 chain1ggm Chain B Residue 2550 [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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PDB1ggm 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)		E188 R220 F230 V232 F235 Q237 E239 E304 L305 E306 R311 E359 S361 G363
Binding residue
(residue number reindexed from 1)		E125 R157 F167 V169 F172 Q174 E176 E241 L242 E243 R248 E296 S298 G300
Annotation score3
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:1ggm, PDBe:1ggm, PDBj:1ggm
PDBsum1ggm
PubMed10064708
UniProtP56206|SYG_THET8 Glycine--tRNA ligase (Gene Name=glyQS)

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