Structure of PDB 1sqf Chain A Binding Site BS01

Receptor Information
>1sqf Chain A (length=425) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNLRSMAAQAVEQVVEQGQSLSNILPPLQQKVSDKDKALLQELCFGVLRT
LSQLDWLINKLMARPMTGKQRTVHYLIMVGLYQLLYTRIPPHAALAETVE
GAIAIKRPQLKGLINGVLRQFQRQQEELLAEFNASDARYLHPSWLLKRLQ
KAYPEQWQSIVEANNQRPPMWLRINRTHHSRDSWLALLDEAGMKGFPHAD
YPDAVRLETPAPVHALPGFEDGWVTVQDASAQGCMTWLAPQNGEHILDLC
AAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMKATVKQGDG
RYPSQWCGEQQFDRILLDAPCSATGVIRRHPDIKWLRRDRDIPELAQLQS
EILDAIWPHLKTGGTLVYATCSVLPEENSLQIKAFLQRTADAELCETGTP
EQPGKQNLPGAEEGDGFFYAKLIKK
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 chain1sqf Chain A Residue 430 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1sqf The First Structure of an RNA m5C Methyltransferase, Fmu, Provides Insight into Catalytic Mechanism and Specific Binding of RNA Substrate
Resolution2.1 Å
Binding residue
(original residue number in PDB)		C254 A255 A256 P257 G259 K260 D277 I278 R282 D303 G304 D322 P324
Binding residue
(residue number reindexed from 1)		C250 A251 A252 P253 G255 K256 D273 I274 R278 D299 G300 D318 P320
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.176: 16S rRNA (cytosine(967)-C(5))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity
GO:0016434 rRNA (cytosine) methyltransferase activity
Biological Process
GO:0001510 RNA methylation
GO:0006355 regulation of DNA-templated transcription
GO:0006364 rRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0070475 rRNA base methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1sqf, PDBe:1sqf, PDBj:1sqf
PDBsum1sqf
PubMed14656444
UniProtP36929|RSMB_ECOLI Ribosomal RNA small subunit methyltransferase B (Gene Name=rsmB)

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