Structure of PDB 3r9x Chain A Binding Site BS03

Receptor Information
>3r9x Chain A (length=302) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMKVGYVAIVGKPNVGKSTLLNNLLGTKVSIISPKAGTTRMRVLGVKNIP
NEAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGW
RPRDEEIYQNFIKPLNKPVIVVINKIDKIGPAKNVLPLIDEIHKKHPELT
EIVPISALKGANLDELVKTILKYLPEGEPLFPEDMITDLPLRLLAAEIVR
EKAMMLTREEVPTSIAVKINEIKPGDANPNMLVIKGEIIVDRENLKPIII
GKKGQRLKEIGKRARQELELILGRPVYLELWVKVVPDWRRRPEYVRLFGY
AL
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)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)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain3r9x Chain A Residue 402 [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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PDB3r9x The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		N13 G15 K16 S17 T18 S32 G36 T37 T38 G61 N123 K124 D126 K127 S155 A156 L157
Binding residue
(residue number reindexed from 1)		N14 G16 K17 S18 T19 S33 G37 T38 T39 G62 N124 K125 D127 K128 S156 A157 L158
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0019843 rRNA binding
GO:0043024 ribosomal small subunit binding
GO:0070181 small ribosomal subunit rRNA binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3r9x, PDBe:3r9x, PDBj:3r9x
PDBsum3r9x
PubMed21646538
UniProtO67800|ERA_AQUAE GTPase Era (Gene Name=era)

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