Structure of PDB 5gin Chain M Binding Site BS03

Receptor Information
>5gin Chain M (length=227) Species: 2287 (Saccharolobus solfataricus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ITVKQTNMENIYECEFNDGSFRLCTRNLVPNFNVYGERLIKYEGVEYREW
NAFRSKLAGAILKGLKTNPIRKGTKVLYLGAASGTTISHVSDIIELNGKA
YGVEFSPRVVRELLLVAQRRPNIFPLLADARFPQSYKSVVENVDVLYVDI
AQPDQTDIAIYNAKFFLKVNGDMLLVIKARSIDVTKDPKEIYKTEVEKLE
NSNFETIQIINLDPYDKDHAIVLSKYK
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 chain5gin Chain M 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]
PDB5gin Box C/D guide RNAs recognize a maximum of 10 nt of substrates
Resolution3.308 Å
Binding residue
(original residue number in PDB)		Y82 G84 A86 T90 E108 F109 A134 D153 I154 A155
Binding residue
(residue number reindexed from 1)		Y78 G80 A82 T86 E104 F105 A130 D149 I150 A151
Annotation score4
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0016740 transferase activity
GO:1990259 histone H2AQ104 methyltransferase activity
Biological Process
GO:0000494 box C/D sno(s)RNA 3'-end processing
GO:0006338 chromatin remodeling
GO:0006364 rRNA processing
GO:0008033 tRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
Cellular Component
GO:0031428 box C/D methylation guide snoRNP complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5gin, PDBe:5gin, PDBj:5gin
PDBsum5gin
PubMed27625427
UniProtP58032|FLPA_SACS2 Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase (Gene Name=flpA)

[Back to BioLiP]