Structure of PDB 5ot7 Chain U Binding Site BS03

Receptor Information
>5ot7 Chain U (length=661) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRITAAVTTCFWKDHRI
NIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYK
VPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIID
VLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIML
KYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDY
LPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIR
VYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVG
LKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALA
RLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKP
QVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAI
VGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSE
MAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRG
QILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEV
PKQVQEKLIKG
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 chain5ot7 Chain U Residue 702 [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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PDB5ot7 The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		I21 D22 A23 G24 T26 T27 K138 K141 S262 L264
Binding residue
(residue number reindexed from 1)		I18 D19 A20 G21 T23 T24 K109 K112 S233 L235
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0032790 ribosome disassembly
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ot7, PDBe:5ot7, PDBj:5ot7
PDBsum5ot7
PubMed29408956
UniProtQ5SHN5|EFG_THET8 Elongation factor G (Gene Name=fusA)

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