Structure of PDB 3axz Chain A Binding Site BS01

Receptor Information
>3axz Chain A (length=241) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFD
KHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKL
DQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELP
AMTLIDAVARFIPGVLADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIR
KWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand IDADN
InChIInChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKeyOIRDTQYFTABQOQ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
FormulaC10 H13 N5 O4
NameADENOSINE
ChEMBLCHEMBL477
DrugBankDB00640
ZINCZINC000002169830
PDB chain3axz Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3axz Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		Y86 L87 S88 P89 G113 L138 G140 P144
Binding residue
(residue number reindexed from 1)		Y92 L93 S94 P95 G119 L144 G146 P150
Annotation score2
Binding affinityMOAD: Kd=372uM
PDBbind-CN: -logKd/Ki=3.43,Kd=372uM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154
Catalytic site (residue number reindexed from 1) P95 E122 R160
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0052906 tRNA (guanine(37)-N1)-methyltransferase activity
Biological Process
GO:0002939 tRNA N1-guanine methylation
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3axz, PDBe:3axz, PDBj:3axz
PDBsum3axz
PubMed21602303
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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