Structure of PDB 5erg Chain B Binding Site BS01

Receptor Information
>5erg Chain B (length=324) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NCFSGYKDLIKEGDLTLIWVSRDNIKPVRMHSEEVFNTRYGSFPHKDIIG
KPYGSQIAIRTFAFVHVLQPTPELWTLSLPHRTQIVYTPDSSYIMQRLNC
SPHSRVIEAGTGSGSFSHAFARSVGHLFSFEFHHIRYEQALEEFKEHGLI
DDNVTITHRDVCQGGFLIKKGDTTSYEFGNNETAASLNANVVFLDLPAPW
DAIPHLDSVISVDEKVGLCCFSPCIEQVDKTLDVLEKYGWTDVEMVEIQG
RQYESRRQMVRSLNDALERLRDIKRHKIKEGDSNYKWKEVTKMEAEIKSH
TSYLTFAFKVVNRSRDDEKVNEIL
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain5erg Chain B Residue 401 [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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PDB5erg Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae.
Resolution2.202 Å
Binding residue
(original residue number in PDB)		Q92 V94 G118 G120 S121 S123 F124 E139 F140 R144 R167 D168 V169 D203 L204 P205
Binding residue
(residue number reindexed from 1)		Q84 V86 G110 G112 S113 S115 F116 E131 F132 R136 R159 D160 V161 D195 L196 P197
Annotation score5
Binding affinityMOAD: Kd=44.33uM
PDBbind-CN: -logKd/Ki=4.35,Kd=44.33uM
Enzymatic activity
Enzyme Commision number 2.1.1.220: tRNA (adenine(58)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0160107 tRNA (adenine(58)-N1)-methyltransferase activity
Biological Process
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
Cellular Component
GO:0005634 nucleus
GO:0031515 tRNA (m1A) methyltransferase complex

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5erg, PDBe:5erg, PDBj:5erg
PDBsum5erg
PubMed27582183
UniProtP46959|TRM61_YEAST tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61 (Gene Name=GCD14)

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