Structure of PDB 5zvh Chain B Binding Site BS01

Receptor Information
>5zvh Chain B (length=384) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLEAFPKELREYYKNLFGKEEANKIMKKLREPVEHYYIRVNTLKISREKL
IGELKKEGLKPLRSPYLPEGLYFVREGPNFSDDFEPKLPVVVANKYAAES
VYQGAMLYAPGVLKADKNIKEGDEVQIRDPKGLLVGIGIARMDYKEMTEA
TRGLAVEVTLPKFKLPSLSELKAFEKGYFYPQGLPSMVTARVLEPKEDDV
IIDMAAAPGGKTTHIAQLLENKGEIIAIDKSKNRLRKMEENIKRLGVKNV
KLVQMDARKLPDLGIKADKILLDAPCTALGVRPKLWEERTLKHIEATARY
QRAFIWAAIKSLRRGGVLVYSTCTLSYEENEGNVKFMIRKGMKLEEQSIF
IGSPGIGMNKVQRFYPHKHLTQGFFIAKLRKVKD
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 chain5zvh 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

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PDB5zvh Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		A209 A210 A211 P212 G214 K215 D233 K234 R238 D260 A261 D277 Y304 F308
Binding residue
(residue number reindexed from 1)		A205 A206 A207 P208 G210 K211 D229 K230 R234 D256 A257 D273 Y300 F304
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
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:0006400 tRNA modification
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5zvh, PDBe:5zvh, PDBj:5zvh
PDBsum5zvh
PubMed30541086
UniProtO57712|NSUN6_PYRHO tRNA (cytosine(72)-C(5))-methyltransferase (Gene Name=PH1991)

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