Structure of PDB 5lzb Chain z Binding Site BS05

Receptor Information
>5lzb Chain z (length=614) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIIATAGHVDHGKTTLLQAITGVNADRLPEEKKRGMTIDLGYAYWPQPDG
RVPGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQ
LTGNPMLTVALTKADRVDEARVDEVERQVKEVLREYGFAEAKLFITAATE
GRGMDALREHLLQLPEREHASQHSFRLAIDRAFTVKGAGLVVTGTALSGE
VKVGDSLWLTGVNKPMRVRALHAQNQPTETANAGQRIALNIAGDAEKEQI
NRGDWLLADVPPEPFTRVIVELQTHTPLTQWQPLHIHHAASHVTGRVSLL
EDNLAELVFDTPLWLADNDRLVLRDISARNTLAGARVVMLNPPRRGKRKP
EYLQWLASLARAQSDADALSVHLERGAVNLADFAWARQLNGEGMRELLQQ
PGYIQAGYSLLNAPVAARWQRKILDTLATYHEQHRDEPGPGRERLRRMAL
PMEDEALVLLLIEKMRESGDIHSHHGWLHLPDHKAGFSEEQQAIWQKAEP
LFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRI
VEFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRG
NDHLLRDALLFPEK
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain5lzb Chain z Residue 701 [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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PDB5lzb The pathway to GTPase activation of elongation factor SelB on the ribosome.
Resolution5.3 Å
Binding residue
(original residue number in PDB)		D10 G12 K13 T14 T15 T37 D57 K113 D115 R116 A147 A148 T149
Binding residue
(residue number reindexed from 1)		D10 G12 K13 T14 T15 T37 D57 K113 D115 R116 A147 A148 T149
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K13 T14 T37 H61
Catalytic site (residue number reindexed from 1) K13 T14 T37 H61
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0019003 GDP binding
GO:0032561 guanyl ribonucleotide binding
GO:0035368 selenocysteine insertion sequence binding
GO:0043168 anion binding
Biological Process
GO:0001514 selenocysteine incorporation
GO:0006412 translation
GO:0016259 selenocysteine metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5lzb, PDBe:5lzb, PDBj:5lzb
PDBsum5lzb
PubMed27842381
UniProtP14081|SELB_ECOLI Selenocysteine-specific elongation factor (Gene Name=selB)

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