Structure of PDB 5zw3 Chain B Binding Site BS01

Receptor Information
>5zw3 Chain B (length=193) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRYEQINDYIEALLKPRPDNVKRLEAYAEEHHVPIMEKAGMEVLLQILSV
KQPKKILEIGTAIGYSAIRMALELPSAEIYTIERNEKRHEEAVNNIKEFQ
LDDRIHVFYGDALELADAVHVTAPYDVIFIDAAKGQYQNFFHLYEPMLSP
DGVIITDNVLFIDEYNHWLMNHPDYQTAIIPVGDGLAISKKKR
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 chain5zw3 Chain B Residue 301 [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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PDB5zw3 Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		P36 I37 M38 G62 A64 Y67 S68 E85 R86 R90 D113 A114 D133 A134 A135 F142
Binding residue
(residue number reindexed from 1)		P34 I35 M36 G60 A62 Y65 S66 E83 R84 R88 D111 A112 D131 A132 A133 F140
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008168 methyltransferase activity
GO:0008171 O-methyltransferase activity
GO:0016300 tRNA (uridine) methyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5zw3, PDBe:5zw3, PDBj:5zw3
PDBsum5zw3
PubMed29982645
UniProtO32036|TRMR_BACSU tRNA 5-hydroxyuridine methyltransferase (Gene Name=trmR)

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