Structure of PDB 2rcn Chain A Binding Site BS02

Receptor Information
>2rcn Chain A (length=278) Species: 99287 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LFGEPAEGIVISRFGMHADVESADGEVHRCNIRRTIRSLVTGDRVVWRPG
KVKGIVEAVHERTSVLTRPVKPIAANIDQIVIVSAILPELSLNIIDRYLV
GCETLQVEPLIVLNKIDLLDDEGMDFVNEQMDIYRNIGYRVLMVSSHTQD
GLKPLEEALTGRISIFAGQSGVGKSSLLNALLGLQNEILTNTAARLYHFP
HGGDVIDSPGVREFGLWHLEPEQITQGFVEFHDYLGHCKYRDCKHDADPG
CAIREAVENGAIAETRFENYHRILESMA
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 chain2rcn Chain A Residue 600 [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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PDB2rcn Structure of the ribosomal interacting GTPase YjeQ from the enterobacterial species Salmonella typhimurium.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		N168 K169 D171 L172 S199 S200 H201 G225 V226 G227 K228 S229 S230
Binding residue
(residue number reindexed from 1)		N114 K115 D117 L118 S145 S146 H147 G171 V172 G173 K174 S175 S176
Annotation score4
Binding affinityMOAD: Kd=1uM
PDBbind-CN: -logKd/Ki=6.00,Kd=1.0uM
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019843 rRNA binding
GO:0046872 metal ion binding
Biological Process
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
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:2rcn, PDBe:2rcn, PDBj:2rcn
PDBsum2rcn
PubMed18007041
UniProtQ8ZKB0|RSGA_SALTY Small ribosomal subunit biogenesis GTPase RsgA (Gene Name=rsgA)

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