Structure of PDB 3vqt Chain C Binding Site BS01

Receptor Information
>3vqt Chain C (length=491) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKAVTTS
VMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQT
RKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPI
GMGSSFKGTYDLLHKQLHLFIQSGIVIHGADDPQLDEYLGDQAEQLRMDL
ALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQP
RPAATRVVEPGEEAFTGVVFKIQRMAFLRICSGTFTRGMRLKHHRTGKDV
TVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVG
IPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILG
AVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYH
RGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREIS
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 chain3vqt Chain C Residue 601 [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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PDB3vqt Crystal structure analysis of the translation factor RF3 (release factor 3)
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D22 G24 K25 T26 T27 H91 N141 K142 D144 S256 I258
Binding residue
(residue number reindexed from 1)		D21 G23 K24 T25 T26 H69 N119 K120 D122 S227 I229
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D22
Catalytic site (residue number reindexed from 1) D21
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016149 translation release factor activity, codon specific
GO:0016150 translation release factor activity, codon nonspecific
Biological Process
GO:0006412 translation
GO:0006415 translational termination
GO:0006449 regulation of translational termination
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:3vqt, PDBe:3vqt, PDBj:3vqt
PDBsum3vqt
PubMed22975312
UniProtB8DIL5|RF3_NITV9 Peptide chain release factor 3 (Gene Name=prfC)

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