Structure of PDB 3v97 Chain B Binding Site BS04

Receptor Information
>3v97 Chain B (length=641) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNSLFASTARGLEELLKTELENLGAVECQVVQGGVHFKGDTRLVYQSLMW
SRLASRIMLPLGECKVYSDLDLYLGVQAINWTEMFNPGATFAVHRNSQYG
AMKVKDAIVDAFTRPRPNVDRDAPDIRVNVWSIALDLSGDGLHLRGYRDI
APIKETLAAAIVMRSGWQPGTPLLDPMCGSGTLLIEAAMLATDRAPGLHR
GRWGFSGWAQHDEAIWQEVKAEAQTRARKGLAEYSSHFYGSDSDARVIQR
ARTNARLAGIGELITFEVKDVAQLTNPLPKGPYGTVLSNPPYSEPALIAL
HSLLGRIMKNQFGGWNLSLFSASPDLLSCLQLRADKQYKAKNGPLDCVQK
NYHVAESEDYTNRLRKNLKKFEKWARQEGIECYRLYDADLPEYNVAVDRY
ADWVVVQEYAHKARQRLFDIIAATISVLGIAPNKLVLKTREKGEFLEVTE
YNAHLWVNLTDYLDTGLFLDHRIARRMLGQMSKGKDFLNLFSYTGSATVH
AGLGGARSTTTVDMSRTYLEWAERNLRLNGLTGRAHRLIQADCLAWLREA
NEQFDLIFIDPPTFSNAFDVQRDHLALMKDLKRLLRAGGTIMFSNNKRGF
RMDLDGLAKLGLKAQEITQKTLSQDFARNRQIHNCWLITAA
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 chain3v97 Chain B Residue 801 [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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PDB3v97 Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA
Resolution2.2 Å
Binding residue
(original residue number in PDB)		M197 C198 S200 D262 S263 D290 V291 N309
Binding residue
(residue number reindexed from 1)		M177 C178 S180 D242 S243 D270 V271 N289
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.173: 23S rRNA (guanine(2445)-N(2))-methyltransferase.
2.1.1.264: 23S rRNA (guanine(2069)-N(7))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008990 rRNA (guanine-N2-)-methyltransferase activity
GO:0052915 23S rRNA (guanine(2445)-N(2))-methyltransferase activity
GO:0070043 rRNA (guanine-N7-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0070475 rRNA base methylation
GO:0070476 rRNA (guanine-N7)-methylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3v97, PDBe:3v97, PDBj:3v97
PDBsum3v97
PubMed22362734
UniProtP75864|RLMKL_ECOLI Ribosomal RNA large subunit methyltransferase K/L (Gene Name=rlmL)

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