Structure of PDB 2zwa Chain B Binding Site BS01

Receptor Information
>2zwa Chain B (length=683) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTTIKQTNKNVKQERRKKYADLAIQGTNNSSIASKRSVELLYLPKLSSAN
NFQMDKNNKLLEYFKFFVPKKIKRSPCINRGYWLRLFAIRSRLNSIIEQT
PQDKKIVVVNLGCGYDPLPFQLLDTNNIQSQQYHDRVSFIDIDYSDLLKI
KIELIKTIPELSKIIGLSEYVDDSNVDFLTTPKYLARPCDLNDSKMFSTL
LNECQLYDPNVVKVFVAEVSLAYMKPERSDSIIEATSKMENSHFIILEQL
IPKGPFEPFSKQMLAHFKRNDSPLQSVLKYNTIESQVQRFNKLGFAYVNV
GDMFQLWESADEATKKELLKVEPFDELEEFHLFCHHYVLCHATNYKEFAF
TQGFLFDRINLTVDEDYQLLECECPINRKFGDVDVAGNDVFYMGGSNPYR
VNEILQLSIHYDKIDMKNIEVSSSEVPVARMCHTFTTISRNNQLLLIGGR
KAPHQGLSDNWIFDMKTREWSMIKSLSHTRFRHSACSLPDGNVLILGGVT
EGPAMLLYNVTEEIFKDVTPKDEFFQNSLVSAGLEFDPVSKQGIILGGGF
MDQTTVSDKAIIFKYDAENATEPITVIKKLQHPLFQRYGSQIKYITPRKL
LIVGGTSPSGLFDRTNSIISLDPLSETLTSIPISRRIWEDHSLMLAGFSL
VSTSMGTIHIIGGGATCYGFGSVTNVGLKLIAI
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 chain2zwa 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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PDB2zwa Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S34 K38 R88 G115 C116 D146 Y147 C195 D196 L197 E224 V225
Binding residue
(residue number reindexed from 1)		S31 K35 R85 G112 C113 D143 Y144 C189 D190 L191 E218 V219
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2zwa, PDBe:2zwa, PDBj:2zwa
PDBsum2zwa
PubMed19287006
UniProtQ08282|TYW4_YEAST tRNA wybutosine-synthesizing protein 4 (Gene Name=PPM2)

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