Structure of PDB 3cno Chain A Binding Site BS01

Receptor Information
>3cno Chain A (length=227) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RQIKDLLRLVNTVVEVRDARAPFATSAYGVDFSRKETIILLNKVDIADEK
TTKKWVEFFKKQGKRVITTHKGEPRKVLLKKLSFDRLARVLIVGVPNTGK
STIINKLKGKRAGIQWFSLENGVKILDTPGILYKNIFSEDLAAKLLLVGS
LPVERIEDQRIFERAFEIFARSIGIESSFSEFFEDFARKRGLLKKGGVPD
IERALMLFFTEVAQGKAGRVSFERPED
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 chain3cno Chain A Residue 501 [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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PDB3cno Crystal structure of YlqF, a circularly permuted GTPase: Implications for its GTPase activation in 50 S ribosomal subunit assembly
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K55 D57 H82 K83 N109 G111 K112 S113 T114
Binding residue
(residue number reindexed from 1)		K43 D45 H70 K71 N97 G99 K100 S101 T102
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3cno, PDBe:3cno, PDBj:3cno
PDBsum3cno
PubMed18536017
UniProtQ9WZM6|RBGA_THEMA Ribosome biogenesis GTPase A (Gene Name=rbgA)

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