Structure of PDB 5jut Chain DC Binding Site BS05

Receptor Information
>5jut Chain DC (length=824) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAGI
TIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAA
LRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQ
VSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGW
AFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKP
LERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKA
LLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIA
IKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNY
VPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGT
LTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCV
LTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVE
SESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARI
MADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQ
WATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFL
LADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTV
KAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEI
VLAARKRHGMKEEVPGWQEYYDKL
Ligand information
Ligand IDSO1
InChIInChI=1S/C27H42O8/c1-13(2)19-8-16-9-25(11-28)18-7-6-14(3)17(18)10-26(16,27(19,25)24(31)32)12-34-23-21(30)20(29)22(33-5)15(4)35-23/h11,13-23,29-30H,6-10,12H2,1-5H3,(H,31,32)/t14-,15-,16+,17-,18-,19?,20+,21+,22-,23-,25+,26+,27+/m1/s1
InChIKeyDIBGPTPYRVEPSP-OHFCZZTFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1CCC2C1CC3(C4CC(C3(C2(C4)C=O)C(=O)O)C(C)C)COC5C(C(C(C(O5)C)OC)O)O
CACTVS 3.341CO[C@@H]1[C@@H](C)O[C@@H](OC[C@@]23C[C@@H]4[C@H](C)CC[C@H]4[C@]5(C[C@@H]2C[C@H](C(C)C)[C@@]35C(O)=O)C=O)[C@@H](O)[C@@H]1O
CACTVS 3.341CO[CH]1[CH](C)O[CH](OC[C]23C[CH]4[CH](C)CC[CH]4[C]5(C[CH]2C[CH](C(C)C)[C]35C(O)=O)C=O)[CH](O)[CH]1O
ACDLabs 10.04O=C(O)C53C4(COC1OC(C(OC)C(O)C1O)C)CC2C(C)CCC2C3(C=O)CC4CC5C(C)C
OpenEye OEToolkits 1.5.0C[C@@H]1CC[C@@H]2[C@@H]1C[C@@]3([C@H]4CC([C@@]3([C@@]2(C4)C=O)C(=O)O)C(C)C)CO[C@H]5[C@H]([C@@H]([C@@H]([C@H](O5)C)OC)O)O
FormulaC27 H42 O8
Name[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID;
SORDARIN
ChEMBL
DrugBank
ZINC
PDB chain5jut Chain DC Residue 903 [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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PDB5jut Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
Resolution4.0 Å
Binding residue
(original residue number in PDB)
Y521 P727 M796 F798 W801
Binding residue
(residue number reindexed from 1)
Y503 P709 M778 F780 W783
Annotation score1
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:0019843 rRNA binding
GO:0042802 identical protein binding
GO:0043022 ribosome binding
GO:0051087 protein-folding chaperone binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0045901 positive regulation of translational elongation
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:5jut, PDBe:5jut, PDBj:5jut
PDBsum5jut
PubMed27159452
UniProtP32324|EF2_YEAST Elongation factor 2 (Gene Name=EFT1)

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