Structure of PDB 3tm5 Chain B Binding Site BS01

Receptor Information
>3tm5 Chain B (length=368) Species: 186497 (Pyrococcus furiosus DSM 3638) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKFLLTTAQGIEDIAKREVSLLLKKLGISFQIEEKPLGIEGRLLLEAEKA
YYVDEKGRKRELSISTYLNENSRLLHRVIIEIASEKFNGIEKDESEEALK
RIKDFVSSLPVEQFVKVSETFAVRSFRKGDHNITSIDIARTVGEAIFERL
SRFGTPLVNLDHPAVIFRAELIKDVFFLGIDTTGDSSLHKRPWRVYDHPA
HLKASIANAMIELAELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKY
RKHLIGAEMNALAAGVLDKIKFIQGDATQLSQYVDSVDFAISNLPYGLKI
GKKSMIPDLYMKFFNELAKVLEKRGVFITTEKKAIEEAIAENGFEIIHHR
VIGHGGLMVHLYVVKLEH
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 chain3tm5 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3tm5 Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		H198 A200 H201 L202 M225 C226 G227 S228 T230 E248 K249 D276 A277 N293
Binding residue
(residue number reindexed from 1)		H198 A200 H201 L202 M225 C226 G227 S228 T230 E248 K249 D276 A277 N293
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.256: tRNA (guanine(6)-N(2))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0016423 tRNA (guanine) methyltransferase activity
GO:0016740 transferase activity
GO:0160117 tRNA (guanine(6)-N2)-methyltransferase activity
Biological Process
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3tm5, PDBe:3tm5, PDBj:3tm5
PDBsum3tm5
PubMed22362751
UniProtQ8U248|TRM14_PYRFU tRNA (guanine(6)-N2)-methyltransferase (Gene Name=trm14)

[Back to BioLiP]