Structure of PDB 4yvj Chain B Binding Site BS03

Receptor Information
>4yvj Chain B (length=249) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHK
TVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQG
GVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMT
LIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLM
SGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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 chain4yvj Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yvj Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 Q90 G113 R114 Y115 E116 S132 L138 G140 G141 P144
Binding residue
(residue number reindexed from 1)		L90 S91 P92 Q93 G116 R117 Y118 E119 S135 L141 G143 G144 P147
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154 D169
Catalytic site (residue number reindexed from 1) P92 E119 R157 D172
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0052906 tRNA (guanine(37)-N1)-methyltransferase activity
Biological Process
GO:0002939 tRNA N1-guanine methylation
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yvj, PDBe:4yvj, PDBj:4yvj
PDBsum4yvj
PubMed26183229
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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