Structure of PDB 3bbd Chain B Binding Site BS01

Receptor Information
>3bbd Chain B (length=204) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEM
RGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYF
RFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPK
LLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICY
SLSF
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 chain3bbd Chain B Residue 207 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bbd The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		M141 T142 K143 I161 G162 F164 P165 G167 I185 K188 L190 V195
Binding residue
(residue number reindexed from 1)		M140 T141 K142 I160 G161 F163 P164 G166 I184 K187 L189 V194
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0019843 rRNA binding
GO:0042803 protein homodimerization activity
GO:0070037 rRNA (pseudouridine) methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0032259 methylation
GO:0042254 ribosome biogenesis
GO:0070475 rRNA base methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3bbd, PDBe:3bbd, PDBj:3bbd
PDBsum3bbd
PubMed18208838
UniProtQ57977|NEP1_METJA Ribosomal RNA small subunit methyltransferase Nep1 (Gene Name=nep1)

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