Structure of PDB 2yxl Chain A Binding Site BS01

Receptor Information
>2yxl Chain A (length=443) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKLSIPPKGIRAIIEAIRLGEIIKPSQYAKREAFKKHDVEEAWLNRVLTM
IFYDIMKKQGLIDKVIKEIVGVTPLILDPWLRAALRVAVDIALFHDPSSQ
TIKNLRWKASDFISSRTHPYVGMYFWDLLDKIFEYKPNPKNELEELEWKY
LAPSWLIERVKGILGDETEDFFRSVNKRHEWISIRVNTLKANVEEVIGEL
EEDGVEVVRSERVPTILKIKGPYNFDTSSAFNEGKIIVQEEASAVASIVL
DPKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDVDKMRMKRLKDFVK
RMGIKIVKPLVKDARKAPEIIGEEVADKVLLDAPCTSSGTIGKNPELRWR
LREDKINEMSQLQRELLESAARLVKPGGRLLYTTCSIFKEENEKNIRWFL
NVHPEFKLVPLKSPYDPGFLEGTMRAWPHRHSTIGFFYALLEK
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 chain2yxl Chain A Residue 5748 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yxl Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase
Resolution2.55 Å
Binding residue
(original residue number in PDB)		A267 A268 A269 P270 G271 G272 K273 D291 V292 R296 A319 D337 P339
Binding residue
(residue number reindexed from 1)		A262 A263 A264 P265 G266 G267 K268 D286 V287 R291 A314 D332 P334
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0016428 tRNA (cytidine-5-)-methyltransferase activity
GO:0016740 transferase activity
Biological Process
GO:0001510 RNA methylation
GO:0006396 RNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2yxl, PDBe:2yxl, PDBj:2yxl
PDBsum2yxl
PubMed21123870
UniProtO58581

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