Structure of PDB 3a4t Chain B Binding Site BS01

Receptor Information
>3a4t Chain B (length=253) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPE
YLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKG
TIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDK
ILLDAPCSGNDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEE
VIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKL
RKI
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 chain3a4t Chain B Residue 501 [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]
PDB3a4t Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		C91 A92 A93 P94 G96 K97 E115 I116 R120 M143 D163 P165 R189
Binding residue
(residue number reindexed from 1)		C82 A83 A84 P85 G87 K88 E106 I107 R111 M134 D154 P156 R168
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.-
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: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:3a4t, PDBe:3a4t, PDBj:3a4t
PDBsum3a4t
PubMed20600111
UniProtQ60343|TRM4_METJA tRNA (cytosine(48)-C(5))-methyltransferase (Gene Name=trm4)

[Back to BioLiP]