Structure of PDB 2zw9 Chain B Binding Site BS01

Receptor Information
>2zw9 Chain B (length=664) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YADLAIQGTNNSSIASKRSVELLYLPKLSSANNFQMDKNNKLLEYFKFFV
PKKIKRSPCINRGYWLRLFAIRSRLNSIIEQTPQDKKIVVVNLGCGYDPL
PFQLLDTNNIQSQQYHDRVSFIDIDYSDLLKIKIELIKTIPELSKIIGLS
NVDFLTTPKYLARPCDLNDSKMFSTLLNECQLYDPNVVKVFVAEVSLAYM
KPERSDSIIEATSKMENSHFIILEQLIPKGPFEPFSKQMLAHFKRNDSPL
QSVLKYNTIESQVQRFNKLGFAYVNVGDMFQLWESADEATKKELLKVEPF
DELEEFHLFCHHYVLCHATNYKEFAFTQGFLFDRSISEINLTVDEDYQLL
ECECPINRKFGDVDVAGNDVFYMGGSNPYRVNEILQLSIHYDKIDMKNIE
VSSSEVPVARMCHTFTTISRNNQLLLIGGRKAPHQGLSDNWIFDMKTREW
SMIKSLSHTRFRHSACSLPDGNVLILGGVTEGPAMLLYNVTEEIFKDVTP
KDEFFQNSLVSAGLEFDPVSKQGIILGGGFMDQTTVSDKAIIFKYDAENA
TEPITVIKKLQHPLFQRYGSQIKYITPRKLLIVGGTSPSGLFDRTNSIIS
LDPLSETLTSIPISRRIWEDHSLMLAGFSLVSTSMGTIHIIGGGATCYGF
GSVTNVGLKLIAIA
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 chain2zw9 Chain B Residue 801 [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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PDB2zw9 Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I27 T30 N31 S34 K38 G115 C116 D146 Y147 C195 L197 E224 V225
Binding residue
(residue number reindexed from 1)		I6 T9 N10 S13 K17 G94 C95 D125 Y126 C165 L167 E194 V195
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.290: tRNA(Phe) [7-(3-amino-3-carboxypropyl)wyosine(37)-O]-methyltransferase.
2.3.1.231: tRNA(Phe) {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine(37)-N}- methoxycarbonyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008175 tRNA methyltransferase activity
Biological Process
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0031591 wybutosine biosynthetic process
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2zw9, PDBe:2zw9, PDBj:2zw9
PDBsum2zw9
PubMed19287006
UniProtQ08282|TYW4_YEAST tRNA wybutosine-synthesizing protein 4 (Gene Name=PPM2)

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