Structure of PDB 1kk3 Chain A Binding Site BS02

Receptor Information
>1kk3 Chain A (length=398) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRQAEVNIGMVGHVDHGKTTLTKALTGVWTDSEELRRGITIKIGFADAEI
RRCPNCGRYSTSPVCPYCGHETEFVRRVSFIDAPGHEALMTTMLAGASLM
DGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALE
NYRQIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDFIPTPKRDPNK
PPKMLVLRSFDVNKPGEKLVGGVLGGSIVQGKLKVGDEIEIRPGVPYEEH
GRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGVGTKLDPYLTKGDLMAGN
VVGKPGKLPPVWDSLRLEVHLLERVVEQELKVEPIKRKEVLLLNVGTART
MGLVTGLGKDEIEVKLQIPVCAEPGDRVAISRQIGSRWRLIGYGIIKE
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 chain1kk3 Chain A Residue 412 [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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PDB1kk3 The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D20 G22 K23 T24 T25 N145 K146 E148 L149 S180 L182
Binding residue
(residue number reindexed from 1)		D15 G17 K18 T19 T20 N138 K139 E141 L142 S173 L175
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D20 K23 T24 T47 H93
Catalytic site (residue number reindexed from 1) D15 K18 T19 T40 H86
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: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
Cellular Component
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:1kk3, PDBe:1kk3, PDBj:1kk3
PDBsum1kk3
PubMed11927566
UniProtQ9V1G0|IF2G_PYRAB Translation initiation factor 2 subunit gamma (Gene Name=eif2g)

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