Structure of PDB 5a9x Chain A Binding Site BS01

Receptor Information
>5a9x Chain A (length=556) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEKLRNIAIIAHVDHGKTTLVDKLLQQSGKERGITILAKNTADYRINIV
DTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKP
IVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGLDH
EDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRI
KRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAI
TELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSR
QILDRLNKELVHNVALRVEETEDADAFRVSGRGELHLSVLIENMRREGFE
LAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKGDLKNM
NPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDDVRPGE
VGQRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSR
SNDLTVNCLTLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKRHLTEND
RRRANR
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5a9x 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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PDB5a9x Structure of Bipa in GTP Form Bound to the Ratcheted Ribosome.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		H16 G17 K18 T19 T20 N128 K129 S166 A167
Binding residue
(residue number reindexed from 1)		H16 G17 K18 T19 T20 N105 K106 S143 A144
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D15 K18 T19 T55 H78
Catalytic site (residue number reindexed from 1) D15 K18 T19 T36 H55
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5a9x, PDBe:5a9x, PDBj:5a9x
PDBsum5a9x
PubMed26283392
UniProtP0A3B2|BIPA_ECO27 Large ribosomal subunit assembly factor BipA (Gene Name=bipA)

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