Structure of PDB 3wy9 Chain B Binding Site BS03

Receptor Information
>3wy9 Chain B (length=416) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPHVNIVFIGHVDHGKSTTIGRLLYDTGNIPETIIKKFESFKFAWVMDRL
KEERERGITIDVAHTKFETPHRYITIIDAPGHRDFVKNMITGASQADAAV
LVVAATDGVMPQTKEHAFLARTLGIKHIIVTINKMDMVNYDQKVFEKVKA
QVEKLLKTLGYKDFPVIPTSAWNGDNVVKKSDKMPWYNGPTLIEALDQIP
EPEKPIDKPLRIPIQDVYSIKGVGTVPVGRVETGKLKVGDVVIFEPASTI
FHKPIQGEVKSIEMHHEPLQEALPGDNIGFNVRGVSKNDIKRGDVAGHTD
KPPTVVRTKDTFKAQIIVLNHPTAITVGYSPVLHAHTAQIPVRFEQILAK
VDPRTGNIVEENPQFIKTGDSAIVVLRPMKPVVLEPVKEIPQLGRFAIRD
MGMTIAAGMVISIQKG
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 chain3wy9 Chain B Residue 500 [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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PDB3wy9 Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1 alpha.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D17 G19 K20 S21 T22 N144 K145 D147 M148 S181 W183
Binding residue
(residue number reindexed from 1)		D13 G15 K16 S17 T18 N133 K134 D136 M137 S170 W172
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D17 K20 S21 T70 H93
Catalytic site (residue number reindexed from 1) D13 K16 S17 T59 H82
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
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:3wy9, PDBe:3wy9, PDBj:3wy9
PDBsum3wy9
PubMed25428348
UniProtO59153|EF1A_PYRHO Elongation factor 1-alpha (Gene Name=tuf)

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