Structure of PDB 3tr5 Chain C Binding Site BS02

Receptor Information
>3tr5 Chain C (length=507) Species: 777 (Coxiella burnetii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VEKQTAMRRTFAIISHPDAGKTTLTEKLLLFGGAIQLAGTIKSRHATSDW
MELEKQVTTSVMQFPYKDYLINLLDTPGHADFTEDTYRTLTAVDSALMVI
DAAKGVEPRTIKLMEVCRLRHTPIMTFINKMDRDTRPSIELLDEIESILR
IHCAPVTWPIGMGKYFKGIYHLIEDAIYLYQPSERIEGINNPELDKKLGD
LASELRNEIELVKGASHPFEREGYLKGELTPIFFGSAINNFGVGELLDAF
VKEAPPPQGRETNSRLVKPEEEKFSGFVFKIQANMDPGHRDRIAFLRIAS
GQYQKGMKAYHVRLKKEIQINNALTFMAGKRENAEEAWPGDIIGLHNHGT
IQIGDTFTQGERFKFTGIPNFASELFRLVRLKDPLKQKALLKGLTQLSEE
GATQLFRPLDSNELILGAVGLLQFDVVAYRLENEYNVKCVYESVNVVTAR
WVICDDKAVLERFNQEQSRNLAYDGGGHLTYLAPSRVNLEITMEKWPEIQ
FSETREH
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 chain3tr5 Chain C Residue 527 [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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PDB3tr5 Structural genomics for drug design against the pathogen Coxiella burnetii.
Resolution2.11 Å
Binding residue
(original residue number in PDB)		D20 G22 K23 T24 T25 H89 K140 D142 R143 S254 I256
Binding residue
(residue number reindexed from 1)		D18 G20 K21 T22 T23 H79 K130 D132 R133 S236 I238
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D20
Catalytic site (residue number reindexed from 1) D18
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
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006412 translation
GO:0006415 translational termination
GO:0006449 regulation of translational termination
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3tr5, PDBe:3tr5, PDBj:3tr5
PDBsum3tr5
PubMed26033498
UniProtQ83DC7|RF3_COXBU Peptide chain release factor 3 (Gene Name=prfC)

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