Structure of PDB 5twj Chain D Binding Site BS01

Receptor Information
>5twj Chain D (length=157) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHVKLQLVAVGTKMPDWVQTGFTEYLRRFPKDMPFELIEIPAGKRGKNAD
IKRILDKEGEQMLAAAGKNRIVTLDIPGKPWDTPQLAAELERWKLDGRDV
SLLIGGPEGLSPACKAAAEQSWSLSALTLPHPLVRVLVAESLYRAWSITT
NHPYHRE
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain5twj Chain D Residue 201 [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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PDB5twj Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine.
Resolution2.299 Å
Binding residue
(original residue number in PDB)		L72 D73 I74 G103 G107 L122 L127 V132
Binding residue
(residue number reindexed from 1)		L74 D75 I76 G105 G109 L124 L129 V134
Annotation score5
Binding affinityMOAD: Kd=5.58uM
PDBbind-CN: -logKd/Ki=5.25,Kd=5.58uM
Enzymatic activity
Enzyme Commision number 2.1.1.177: 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0042803 protein homodimerization activity
GO:0043022 ribosome binding
GO:0070038 rRNA (pseudouridine-N3-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0070475 rRNA base methylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5twj, PDBe:5twj, PDBj:5twj
PDBsum5twj
PubMed28428565
UniProtP0A8I8|RLMH_ECOLI Ribosomal RNA large subunit methyltransferase H (Gene Name=rlmH)

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