Structure of PDB 5a9y Chain A Binding Site BS01

Receptor Information
>5a9y Chain A (length=562) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFKERGITILAKNTANDYRI
NIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYG
LKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNG
LDHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGI
GRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDI
VAITELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFV
TSRQILDRLNKELVHNVALRVEETEDADAFRVSGRGELHLSVLIENMRRE
GFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKGDL
KNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDDVR
PGEVGQRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGI
HSRSNDLTVNCLTAVVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKR
HLTENDRRRANR
Ligand information
Ligand IDG4P
InChIInChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyBUFLLCUFNHESEH-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H17 N5 O17 P4
NameGUANOSINE-5',3'-TETRAPHOSPHATE;
guanosine tetraphosphate;
ppGpp
ChEMBL
DrugBankDB04022
ZINCZINC000008217069
PDB chain5a9y Chain A Residue 1603 [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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PDB5a9y Structure of Bipa in GTP Form Bound to the Ratcheted Ribosome.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		H16 G17 K18 T19 T20 N128 K129 D131 R132 A167
Binding residue
(residue number reindexed from 1)		H16 G17 K18 T19 T20 N108 K109 D111 R112 A147
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D15 K18 T19 T55 H78
Catalytic site (residue number reindexed from 1) D15 K18 T19 T38 H58
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019843 rRNA binding
GO:0043022 ribosome binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5a9y, PDBe:5a9y, PDBj:5a9y
PDBsum5a9y
PubMed26283392
UniProtP0A3B2|BIPA_ECO27 Large ribosomal subunit assembly factor BipA (Gene Name=bipA)

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