Structure of PDB 2h5e Chain A Binding Site BS01

Receptor Information
>2h5e Chain A (length=488) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQITTSVMQFPYHDCL
VNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLR
DTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVY
HLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELEL
VKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQ
TDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLRQ
VRTAKDVVISDALTFMAVEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFT
GIPNFAPELFRRIRLKDPKQLLKGLVQLSEEGAVQVFRPISNNDLIVGAV
GVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNES
QLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH
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 chain2h5e Chain A Residue 2567 [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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PDB2h5e RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D23 G25 K26 T27 T28 H92 N142 K143 D145 T258 L260
Binding residue
(residue number reindexed from 1)		D21 G23 K24 T25 T26 H59 N109 K110 D112 T225 L227
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=8.25,Kd=5.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D23
Catalytic site (residue number reindexed from 1) D21
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016149 translation release factor activity, codon specific
GO:0016150 translation release factor activity, codon nonspecific
GO:0019003 GDP binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006412 translation
GO:0006415 translational termination
GO:0006449 regulation of translational termination
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2h5e, PDBe:2h5e, PDBj:2h5e
PDBsum2h5e
PubMed17540173
UniProtP0A7I4|RF3_ECOLI Peptide chain release factor RF3 (Gene Name=prfC)

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