Structure of PDB 2bh2 Chain A Binding Site BS02

Receptor Information
>2bh2 Chain A (length=418) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARA
KVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKH
DVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPI
LAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSA
DREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFI
QVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGV
EGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDP
ARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAML
DMFPHTGHLESMVLFSRV
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 chain2bh2 Chain A Residue 500 [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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PDB2bh2 A Unique RNA Fold in the Ruma-RNA-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function
Resolution2.15 Å
Binding residue
(original residue number in PDB)		F263 Q265 F294 C295 N299 E315 G316 E341 N342 L343 E344 D363
Binding residue
(residue number reindexed from 1)		F249 Q251 F280 C281 N285 E301 G302 E327 N328 L329 E330 D349
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.190: 23S rRNA (uracil(1939)-C(5))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005506 iron ion binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0070041 rRNA (uridine-C5-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0009451 RNA modification
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0070475 rRNA base methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2bh2, PDBe:2bh2, PDBj:2bh2
PDBsum2bh2
PubMed15766524
UniProtP55135|RLMD_ECOLI 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (Gene Name=rlmD)

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