Structure of PDB 3wnc Chain A Binding Site BS01

Receptor Information
>3wnc Chain A (length=361) Species: 2209 (Methanosarcina mazei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HSSGLVPRGSHMANVAIIGTEKSGRTSLAANLGKKGTSSDITMYNNDKEG
RNMVFVDAHSYPKTLKSLITALNISDIAVLCIPPQGLDAHTGECIIALDL
LGFKHGIIALTRSDSTHMHAIDELKAKLKVITSGTVLQDWECISLNTNKS
AKNPFEGVDELKARINEVAEKIEAENAELNSLPARIFIDHAFNVTGKGCV
VLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVGMRL
KNVQAKDIERGFIISDKEIVTTDYTLECTVSKFTKKIEPASVLHLFVGLQ
SEPVRVEKILVDGNEVEEAKPGSTCVLELSGNKKLAYSKQDRFLLANLDL
TQRFAAYGFSK
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 chain3wnc Chain A Residue 401 [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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PDB3wnc A SelB/EF-Tu/aIF2 gamma-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.).
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S12 G13 R14 T15 S16 R101 D103 N135 T136
Binding residue
(residue number reindexed from 1)		S23 G24 R25 T26 S27 R112 D114 N146 T147
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
Biological Process
GO:0001514 selenocysteine incorporation
GO:0006414 translational elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3wnc, PDBe:3wnc, PDBj:3wnc
PDBsum3wnc
PubMed25618148
UniProtQ8PXB3

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