Structure of PDB 5jut Chain DC Binding Site BS04

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 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 chain5jut Chain DC Residue 901 [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)		H27 V28 G31 K32 S33 T34 G67 K159 L215
Binding residue
(residue number reindexed from 1)		H26 V27 G30 K31 S32 T33 G49 K141 L197
Annotation score4
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
View graph for
Biological Process
View graph for
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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