Structure of PDB 3kt3 Chain B Binding Site BS01

Receptor Information
>3kt3 Chain B (length=405) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVKEQVVTPWDVEGGVDEQGRAQNIDYDKLIKQFGTKPVNEETLKRFKQV
TGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGH
MIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDI
IAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDC
IGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVA
DKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINK
YAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGE
LLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERL
VAPKP
Ligand information
Ligand IDTYM
InChIInChI=1S/C21H24N7O8P/c22-12(5-10-6-24-13-4-2-1-3-11(10)13)21(31)36-37(32,33)34-7-14-16(29)17(30)20(35-14)28-9-27-15-18(23)25-8-26-19(15)28/h1-4,6,8-9,12,14,16-17,20,24,29-30H,5,7,22H2,(H,32,33)(H2,23,25,26)/t12-,14+,16+,17+,20+/m0/s1
InChIKeyIFQVDHDRFCKAAW-SQIXAUHQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](Cc1c[nH]c2ccccc12)C(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)CC(C(=O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N
ACDLabs 10.04O=C(OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc5c4ccccc4nc5
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N
CACTVS 3.341N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
FormulaC21 H24 N7 O8 P
NameTRYPTOPHANYL-5'AMP
ChEMBL
DrugBankDB01831
ZINCZINC000016051386
PDB chain3kt3 Chain B Residue 700 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kt3 Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design
Resolution2.6 Å
Binding residue
(original residue number in PDB)		Y106 T107 G108 R109 G110 G119 H120 P123 E141 T143 E146 K147 Q230 C255 A256 D258 Q259 F263 F286 K295 M296
Binding residue
(residue number reindexed from 1)		Y86 T87 G88 R89 G90 G99 H100 P103 E121 T123 E126 K127 Q210 C235 A236 D238 Q239 F243 F266 K275 M276
Annotation score2
Enzymatic activity
Enzyme Commision number 6.1.1.2: tryptophan--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004830 tryptophan-tRNA ligase activity
GO:0005524 ATP binding
GO:1990825 sequence-specific mRNA binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-tRNA aminoacylation
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:3kt3, PDBe:3kt3, PDBj:3kt3
PDBsum3kt3
PubMed20123733
UniProtQ12109|SYWC_YEAST Tryptophan--tRNA ligase, cytoplasmic (Gene Name=WRS1)

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