Structure of PDB 5ynq Chain A Binding Site BS01

Receptor Information
>5ynq Chain A (length=291) Species: 1235996 (Human betacoronavirus 2c EMC/2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPVHMNIAKYMQLCQ
YLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNE
FVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFFTY
LCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSS
EGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQL
KLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTD
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 chain5ynq Chain A 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]
PDB5ynq Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex
Resolution1.958 Å
Binding residue
(original residue number in PDB)		N43 Y47 G71 A72 G73 P80 D99 L100 D114 C115 D130 M131 Y132
Binding residue
(residue number reindexed from 1)		N41 Y45 G69 A70 G71 P78 D97 L98 D112 C113 D128 M129 Y130
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.57: methyltransferase cap1.
3.4.19.12: ubiquitinyl hydrolase 1.
3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:5ynq, PDBe:5ynq, PDBj:5ynq
PDBsum5ynq
PubMed
UniProtK0BWD0

[Back to BioLiP]