Structure of PDB 4xbo Chain B Binding Site BS01

Receptor Information
>4xbo Chain B (length=226) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPAAGASDVI
GNAHIVDTLDEALAGCSLVVGTSARSRTLPWPMLDPRECGLKSVAEAANT
PVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVR
MAWLATQENETPYPLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRR
LFTRARPESQELNILRGILASIEQQN
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain4xbo Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xbo tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily
Resolution2.6 Å
Binding residue
(original residue number in PDB)		T79 S80 A81 F113 G114 R115 G119 I134 S142 L143 A148
Binding residue
(residue number reindexed from 1)		T72 S73 A74 F106 G107 R108 G112 I127 S135 L136 A141
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.59,Kd=26uM
Enzymatic activity
Enzyme Commision number 2.1.1.200: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0002128 tRNA nucleoside ribose methylation
GO:0006396 RNA processing
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4xbo, PDBe:4xbo, PDBj:4xbo
PDBsum4xbo
PubMed26202969
UniProtP0AE01|TRMJ_ECOLI tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ (Gene Name=trmJ)

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