Structure of PDB 2v3k Chain A Binding Site BS01

Receptor Information
>2v3k Chain A (length=218) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQAPPVLTSKDKITKRMIVVLAMASLETHKIYVLLNCDDHQGLLKKMGRD
ISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRT
FKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFD
APVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLS
ASVACSKFCHGAEDAWNI
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 chain2v3k Chain A Residue 1254 [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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PDB2v3k The Yeast Ribosome Synthesis Factor Emg1 is a Novel Member of the Superfamily of Alpha/Beta Knot Fold Methyltransferases.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L180 S181 F182 V206 G207 A210 G212 D214 G226 L227 L232
Binding residue
(residue number reindexed from 1)		L147 S148 F149 V173 G174 A177 G179 D181 G193 L194 L199
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.260: rRNA small subunit pseudouridine methyltransferase Nep1.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0019843 rRNA binding
GO:0042802 identical protein binding
GO:0070037 rRNA (pseudouridine) methyltransferase activity
Biological Process
GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0030490 maturation of SSU-rRNA
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0070475 rRNA base methylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005880 nuclear microtubule
GO:0030686 90S preribosome
GO:0032040 small-subunit processome
GO:0034399 nuclear periphery
GO:1990904 ribonucleoprotein complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2v3k, PDBe:2v3k, PDBj:2v3k
PDBsum2v3k
PubMed18063569
UniProtQ06287|NEP1_YEAST Ribosomal RNA small subunit methyltransferase NEP1 (Gene Name=EMG1)

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