Structure of PDB 3a25 Chain A Binding Site BS01

Receptor Information
>3a25 Chain A (length=264) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKPRIREILSKELPEELVKLLPKRWVRIGDVLLLPLRPELEPYKHRIAEV
YAEVLGVKTVLRKGDYELLYGSDTVTVHVENGIKYKLDVAKIMFSPANVK
ERVRMAKVAKPDELVVDMFAGIGHLSLPIAVYGKAKVIAIEKDPYTFKFL
VENIHLNKVEDRMSAYNMDNRDFPGENIADRILMGYVVRTHEFIPKALSI
AKDGAIIHYHNTVPEKLMPREPFETFKRITKEYGYDVEKLNELKIKRYAP
GVWHVVLDLRVFKS
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain3a25 Chain A Residue 279 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3a25 Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2
Resolution2.3 Å
Binding residue
(original residue number in PDB)		M107 S109 F133 G135 H138 E155 K156 D183 N184
Binding residue
(residue number reindexed from 1)		M93 S95 F119 G121 H124 E141 K142 D169 N170
Annotation score5
Enzymatic activity
Enzyme Commision number 2.5.1.114: tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase.
Gene Ontology
Molecular Function
GO:0008175 tRNA methyltransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0102522 tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity
Biological Process
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0031591 wybutosine biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3a25, PDBe:3a25, PDBj:3a25
PDBsum3a25
PubMed19717466
UniProtO58523|TYW2_PYRHO tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase (Gene Name=taw2)

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