Structure of PDB 6i5m Chain A Binding Site BS01

Receptor Information
>6i5m Chain A (length=414) Species: 2287 (Saccharolobus solfataricus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGY
AETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLM
ATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKV
DVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEY
IKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQ
EIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYL
DPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPI
RAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQI
AGRWRMIGWGLVEI
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 chain6i5m Chain A Residue 501 [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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PDB6i5m The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D19 G21 K22 T23 T24 N149 K150 D152 S184 L186
Binding residue
(residue number reindexed from 1)		D18 G20 K21 T22 T23 N148 K149 D151 S183 L185
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D19 K22 T23 T46 H97
Catalytic site (residue number reindexed from 1) D18 K21 T22 T45 H96
Enzyme Commision number 3.6.5.3: protein-synthesizing GTPase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003743 translation initiation factor activity
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0001731 formation of translation preinitiation complex
GO:0006412 translation
GO:0006413 translational initiation
GO:0006414 translational elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6i5m, PDBe:6i5m, PDBj:6i5m
PDBsum6i5m
PubMed30988256
UniProtQ980A5|IF2G_SACS2 Translation initiation factor 2 subunit gamma (Gene Name=eif2g)

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