Structure of PDB 2vs1 Chain A Binding Site BS01

Receptor Information
>2vs1 Chain A (length=398) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMRGVIRKLNDDGFGVLKGILVPFSAPGDEIIVERVERVKKRRVASQW
KLVRSSPLRVKCGGCTLQHLNYDYQLEFKRKKLKRILGFEVEVVPSPKIF
GHRNRIDLAITKDGIGFREKWWKIVDIDECPVFGKTSREAIERLKEFIEE
EKISVWNIKKDEGFLRYMVLREGKFTEEVMVNFVTKEGNLPDPTNYFDFD
SIYWSVNRSKSDVSYGDIERFWGKEFIRERLDDVDYLIHPNSFFQTNSYQ
AVNLVRKVSELVEGEKILDMYSGVGTFGIYLAKRGFNVKGFDSNEFAIEM
ARRNVEINNVDAEFEVASDREVSVKGFDTVIVDPPRAGLHPRLVKRLNRE
KPGVIVYVSCNPETFARDVKMLDYRIDEIVALDMFPHTPHVELVAKLV
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 chain2vs1 Chain A Residue 501 [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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PDB2vs1 The Crystal Structure of Pyrococcus Abyssi tRNA (Uracil-54, C5)-Methyltransferase Provides Insights Into its tRNA Specificity.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F250 Q252 Y278 S279 T283 D299 S300 D326 D340 P342
Binding residue
(residue number reindexed from 1)		F243 Q245 Y271 S272 T276 D292 S293 D319 D333 P335
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) A25
Catalytic site (residue number reindexed from 1) A28
Enzyme Commision number 2.1.1.35: tRNA (uracil(54)-C(5))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0030697 tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006396 RNA processing
GO:0008033 tRNA processing
GO:0009451 RNA modification
GO:0030488 tRNA methylation
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vs1, PDBe:2vs1, PDBj:2vs1
PDBsum2vs1
PubMed18653523
UniProtQ9UZR7|ATRMA_PYRAB tRNA (uracil(54)-C(5))-methyltransferase (Gene Name=PYRAB10780)

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