Structure of PDB 6qe5 Chain A Binding Site BS01

Receptor Information
>6qe5 Chain A (length=270) Species: 1001989 (Escherichia coli PCN033) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLSYRHSFHAGNHADVLKHTVQSLIIESLKEKDKPFLYLDTHAGAGRYQL
GGKYLEGIARIWQQDDLPAELEAYINVVKHFNRSGQLRYYPGSPLIARQL
LREQDSLQLTELHPSDYPLLRSEFQKDSRARVEKADGFQQLKAKLPPVSR
RGLILIDPPYEMKTDYQAVVSGIAEGYKRFATGTYALWYPVVLRQQIKRM
IHDLEATGIRKILQIELAVLPDSGMTASGMIVINPPWKLEQQMNNVLPWL
HSKLVPAGTGHATVSWIVPE
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6qe5 Chain A Residue 301 [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]
PDB6qe5 Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Resolution1.61 Å
Binding residue
(original residue number in PDB)		Y4 H6 K18 H19 H42 A43 G99 S100 E118 L119 D143 G144 D164 P166
Binding residue
(residue number reindexed from 1)		Y4 H6 K18 H19 H42 A43 G92 S93 E111 L112 D136 G137 D157 P159
Annotation score5
Binding affinityMOAD: Kd=7.5uM
PDBbind-CN: -logKd/Ki=5.12,Kd=7.5uM
Enzymatic activity
Enzyme Commision number 2.1.1.266: 23S rRNA (adenine(2030)-N(6))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0008988 rRNA (adenine-N6-)-methyltransferase activity
GO:0036307 23S rRNA (adenine(2030)-N(6))-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0015976 carbon utilization
GO:0032259 methylation
GO:0070475 rRNA base methylation
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6qe5, PDBe:6qe5, PDBj:6qe5
PDBsum6qe5
PubMed30879411
UniProtP37634|RLMJ_ECOLI Ribosomal RNA large subunit methyltransferase J (Gene Name=rlmJ)

[Back to BioLiP]