Structure of PDB 5m1j Chain A6 Binding Site BS02

Receptor Information
>5m1j Chain A6 (length=539) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DMPDFHDEGEFDDYLNDDEYDLMNEVFPTLKAQLQDYQGWDNLSLKLALF
DNNFDLESTLAELKKTVQRYYKTTVPTKPKKPHDISAFVKSALPHLSFVV
LGHVDAGKSTLMGRLLYDLNIVNQSQLRKLQRESETMGKSSFKFAWIMDQ
TNEERERGVTVSICTSHFSTHRANFTIVDAPGHRDFVPNAIMGISQADMA
ILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDWSQ
QRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWY
NGPNLMSTLENAAFKISKENEGINKDDPFLFSVLEIIPSKKTSNDLALVS
GKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQGQSTNHEETDVAIKGD
FVTLKLRKAYPEDIQNGDLAASVDYSSIHSAQCFVLELTTFDMNRPLLPG
TPFILFIGVKEQPARIKRLISFIDKGNTASKKKIRHLGSKQRAFVEIELI
EVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ
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 chain5m1j Chain A6 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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PDB5m1j Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		V176 G179 K180 S181 T182 F214 V231 K314 N317 S352 G353 F354
Binding residue
(residue number reindexed from 1)		V104 G107 K108 S109 T110 F142 V159 K242 N245 S280 G281 F282
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0043022 ribosome binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0006417 regulation of translation
GO:0032790 ribosome disassembly
GO:0045727 positive regulation of translation
GO:0045948 positive regulation of translational initiation
GO:0070651 nonfunctional rRNA decay
GO:0070966 nuclear-transcribed mRNA catabolic process, no-go decay
GO:0072344 rescue of stalled ribosome
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1990533 Dom34-Hbs1 complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m1j, PDBe:5m1j, PDBj:5m1j
PDBsum5m1j
PubMed27995908
UniProtP32769|HBS1_YEAST Elongation factor 1 alpha-like protein (Gene Name=HBS1)

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