Structure of PDB 3vr1 Chain B Binding Site BS01

Receptor Information
>3vr1 Chain B (length=516) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKARKA
ARHATSDWMAMERERGISVTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYR
VLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHP
LDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFSAIQSGIV
IHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFG
SAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQARM
AFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDII
GIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQK
GLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYE
GVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESA
MERYPKVEFRTTREIS
Ligand information
Ligand IDG4P
InChIInChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyBUFLLCUFNHESEH-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=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)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H17 N5 O17 P4
NameGUANOSINE-5',3'-TETRAPHOSPHATE;
guanosine tetraphosphate;
ppGpp
ChEMBL
DrugBankDB04022
ZINCZINC000008217069
PDB chain3vr1 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vr1 Crystal structure analysis of the translation factor RF3 (release factor 3)
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D22 G24 K25 T26 T27 K49 H91 N141 K142 D144 R145 S256 I258
Binding residue
(residue number reindexed from 1)		D22 G24 K25 T26 T27 K49 H91 N141 K142 D144 R145 S251 I253
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D22
Catalytic site (residue number reindexed from 1) D22
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:3vr1, PDBe:3vr1, PDBj:3vr1
PDBsum3vr1
PubMed22975312
UniProtB8DIL5|RF3_NITV9 Peptide chain release factor 3 (Gene Name=prfC)

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