Structure of PDB 4ac9 Chain B Binding Site BS01

Receptor Information
>4ac9 Chain B (length=456) Species: 39152 (Methanococcus maripaludis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDFKNINLGIFGHIDHGKTTLSKVLTEIAKRGITIDIGFSAFKLENYRIT
LVDAPGHADLIRAVVSAADIIDLALIVVDAKEGPKTQTGEHMLILDHFNI
PIIVVITKSDNAGTEEIKRTEMIMKSILQSTHNLKNSSIIPISAKTGFGV
DELKNLIITTLNNAEIIRNTESYFKMPLDHAFPIKGAGTVVTGTINKGIV
KVGDELKVLPINMSTKVRSIQYFKESVMEAKAGDRVGMAIQGVDAKQIYR
GCILTSKDTKLQTVDKIVAKIKISDIFKYNLTPKMKVHLNVGMLIVPAVA
VPFKKVTFGKTEENIILNEVISGNECYCAFELEEKVLAEVGDRVLITRLD
LPPTTLRICGHGLIEEFKPIKDLNIKKEVLREGKVKIDKGRTVIDGLAQS
KVAAEKLIGEEISIEGKDIVGKIKGTFGTKGLLTAEFSGNVENRDKVILN
RLRRWG
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 chain4ac9 Chain B Residue 1469 [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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PDB4ac9 Selenocysteine tRNA-Specific Elongation Factor Selb is a Structural Chimaera of Elongation and Initiation Factors.
Resolution3.03 Å
Binding residue
(original residue number in PDB)		I14 D15 G17 K18 T19 T20 K120 D122 S155 A156 K157
Binding residue
(residue number reindexed from 1)		I14 D15 G17 K18 T19 T20 K108 D110 S143 A144 K145
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D15 K18 T19 T46 H69
Catalytic site (residue number reindexed from 1) D15 K18 T19 T34 H57
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0046872 metal ion binding
Biological Process
GO:0001514 selenocysteine incorporation
GO:0006414 translational elongation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ac9, PDBe:4ac9, PDBj:4ac9
PDBsum4ac9
PubMed15616587
UniProtQ8J307

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