Structure of PDB 2yx1 Chain A Binding Site BS03

Receptor Information
>2yx1 Chain A (length=323) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILK
SILNIEFELVDKELEEKPSFREIISKKYRKEIDEGLISLSYDVVGDLVIL
QISDEVDEKIRKEIGELAYKLIPCKGVFRRKRVRELEHLAGENRTLTIHK
ENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIAC
KNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVI
MNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLE
KRIVKSYAPREYILALDFKINKK
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 chain2yx1 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yx1 Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R186 F203 A204 P208 F209 D223 I224 D251 V252 N265 L266
Binding residue
(residue number reindexed from 1)		R173 F190 A191 P195 F196 D210 I211 D238 V239 N252 L253
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008175 tRNA methyltransferase activity
GO:0016740 transferase activity
GO:0052906 tRNA (guanine(37)-N1)-methyltransferase activity
Biological Process
GO:0002939 tRNA N1-guanine methylation
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yx1, PDBe:2yx1, PDBj:2yx1
PDBsum2yx1
PubMed18384044
UniProtQ58293|TRM5B_METJA tRNA (guanine(37)-N1)-methyltransferase Trm5b (Gene Name=trm5b)

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