Structure of PDB 3gru Chain A Binding Site BS01

Receptor Information
>3gru Chain A (length=263) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCFLIDKNFVNKAVESANLTKDDVVLEIGLGKGILTEELAKNAKKVYVIE
IDKSLEPYANKLKELYNNIEIIWGDALKVDLNKLDFNKVVANLPYQISSP
ITFKLIKRGFDLAVLMYQYEFAKRMVAAAGTKDYGRLSVAVQSRADVEIV
AKVPPSAFYPKPKVYSAIVKIKPNKGKYHIENENFFDDFLRAIFQHRNKS
VRKALIDSSKELNYNKDEMKKILEDFLNTNSEIKNLINEKVFKLSVKDIV
NLSNEFYRFLQNR
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain3gru Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gru Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		E59 I60 D84 A85 P103
Binding residue
(residue number reindexed from 1)		E50 I51 D75 A76 P94
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G38 E59 N101 Y104 F167
Catalytic site (residue number reindexed from 1) G29 E50 N92 Y95 F158
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0016433 rRNA (adenine) methyltransferase activity
GO:0016740 transferase activity
Biological Process
GO:0000154 rRNA modification
GO:0006364 rRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
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:3gru, PDBe:3gru, PDBj:3gru
PDBsum3gru
PubMed20163168
UniProtQ58435|RSMA_METJA Probable ribosomal RNA small subunit methyltransferase A (Gene Name=rsmA)

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