Structure of PDB 3bbh Chain A Binding Site BS01

Receptor Information
>3bbh Chain A (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 IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain3bbh Chain A Residue 206 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bbh The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		M141 T142 K143 G162 F164 S184 I185 Y186 G189 L190 V195
Binding residue
(residue number reindexed from 1)		M140 T141 K142 G161 F163 S183 I184 Y185 G188 L189 V194
Annotation score3
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:3bbh, PDBe:3bbh, PDBj:3bbh
PDBsum3bbh
PubMed18208838
UniProtQ57977|NEP1_METJA Ribosomal RNA small subunit methyltransferase Nep1 (Gene Name=nep1)

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