Structure of PDB 5xj2 Chain B Binding Site BS01

Receptor Information
>5xj2 Chain B (length=452) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLKKNDIVEVEIVDLTHEGAGVAKVDGLVFFVENALPSEKILMRVLKVNK
KIGFGKVEKYLVQSPHRNQDLDLAYLRSGIADLGHLSYPEQLKFKTKQVK
DSLYKIAGIADVEVAETLGMEHPVKYRNKAQVPVRRVNGVLETGFFRKNS
HNLMPLEDFFIQDPVIDQVVVALRDLLRRFDLKPYDEKEQSGLIRNLVVR
RGHYSGQIMVVLVTTRPKVFRVDQLIEQVIKQFPEIVSVMQNINDQNTNA
IFGKEWRTLYGQDYITDQMLGNDFQIAGPAFYQVNTEMAEKLYQTAIDFA
ELKKDDVIIDAYSGIGTIGLSVAKHVKEVYGVELIPEAVENSQKNASLNK
ITNAHYVCDTAENAMKKWLKEGIQPTVILVDPPRKGLTESFIKASAQTGA
DRIAYISCNVATMARDIKLYQELGYELKKVQPVDLFPQTHHVQTVALLSK
LD
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 chain5xj2 Chain B Residue 502 [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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PDB5xj2 Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD
Resolution2.84 Å
Binding residue
(original residue number in PDB)		F281 Y293 Y312 T317 E333 L334 I335 A361 E362 D381
Binding residue
(residue number reindexed from 1)		F281 Y293 Y312 T317 E333 L334 I335 A361 E362 D381
Annotation score4
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0008173 RNA methyltransferase activity
Biological Process
GO:0006396 RNA processing

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5xj2, PDBe:5xj2, PDBj:5xj2
PDBsum5xj2
PubMed28949991
UniProtQ97R12|Y1029_STRPN Uncharacterized RNA methyltransferase SP_1029 (Gene Name=SP_1029)

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