Structure of PDB 4wqf Chain DZ Binding Site BS06

Receptor Information
>4wqf Chain DZ (length=730) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEAR
IRAQAKRLAERKAEAERLKEILENDLKRLRNIGIAAHIDAGKTTTTERIL
YYTGRIHAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFD
SSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGA
RPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQA
REYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVF
LGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPL
AALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMH
ANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVI
DVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHL
EIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGH
VKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFP
VVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVE
VTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDL
RSKTQGRGSFVMFFDHYQEVPKQVQEKLIK
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 chain4wqf Chain DZ Residue 704 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4wqf Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D22 G24 K25 T26 T27 N137 K138 D140 S262 L264
Binding residue
(residue number reindexed from 1)		D89 G91 K92 T93 T94 N178 K179 D181 S303 L305
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
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
GO:0005840 ribosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4wqf, PDBe:4wqf, PDBj:4wqf
PDBsum4wqf
PubMed25594181
UniProtQ5SHN5|EFG_THET8 Elongation factor G (Gene Name=fusA);
Q5SLQ1|RL9_THET8 Large ribosomal subunit protein bL9 (Gene Name=rplI)

[Back to BioLiP]