Structure of PDB 4dmg Chain A Binding Site BS01

Receptor Information
>4dmg Chain A (length=385) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLGPVLRLVVKAGKERKLRNFYPNLYRDEIAAPPEGVGVAEAVDAEGHFL
AVGYYDPRSRVPFRAFRFDPGPLNRAFFQGRFARALRRRQGLGESHRLVH
GEADGLPGLVVDRFGEVLVLQVRSRGMEALREVWLPALLEVVAPKGVYER
SDVEARRQEGLPERVGVVYGEVPEVLEVEEDGLRFPIPLALAQKTGYYLD
QRENRRLFEAMVRPGERVLDVYSYVGGFALRAARKGAYALAVDKDLEALG
VLDQAALRLGLRVDIRHGEALPTLRGLEGPFHHVLLDPPTLVKRPEELPA
MKRHLVDLVREALRLLAEEGFLWLSSCSYHLRLEDLLEVARRAAADLGRR
LRVHRVTYQPEDHPWSLHIPESLYLKTLVLQDDPL
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 chain4dmg Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dmg Identification and Characterization of the Thermus thermophilus 5-Methylcytidine (m5C) Methyltransferase Modifying 23 S Ribosomal RNA (rRNA) Base C1942.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Q193 Y198 R205 Y222 S223 Y224 F228 D243 K244 E269 A270 D287 P289
Binding residue
(residue number reindexed from 1)		Q193 Y198 R205 Y222 S223 Y224 F228 D243 K244 E269 A270 D287 P289
Annotation score4
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 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:4dmg, PDBe:4dmg, PDBj:4dmg
PDBsum4dmg
PubMed22711535
UniProtQ5SI81|RLM0_THET8 Ribosomal RNA large subunit methyltransferase I (Gene Name=RlmO)

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