Structure of PDB 4yye Chain B Binding Site BS04

Receptor Information
>4yye Chain B (length=417) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFG
FNEVVTPLIYKKTLWEKSGHWENYADDMFKVETTDEEKEEYGLKPMNCPG
HCLIFGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHI
FCTPSQVKSEIFNSLKLIDIVYNKIFPSNYFINFSTRPDHFIGDLKVWNH
AEQVLKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLD
FQLPERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFW
LNPYQAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNV
DLDIRNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNKSFEKL
TMSQIWEKFIELEKNYK
Ligand information
Ligand IDTSB
InChIInChI=1S/C14H21N7O8S/c1-5(22)7(15)13(25)20-30(26,27)28-2-6-9(23)10(24)14(29-6)21-4-19-8-11(16)17-3-18-12(8)21/h3-7,9-10,14,22-24H,2,15H2,1H3,(H,20,25)(H2,16,17,18)/t5-,6-,7+,9-,10-,14-/m1/s1
InChIKeyUPVAPSGKXAAHBG-CKTDUXNWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](O)[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341C[C@@H](O)[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CC(C(C(=O)NS(=O)(=O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N)O
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)C(O)C
OpenEye OEToolkits 1.5.0C[C@H]([C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N)O
FormulaC14 H21 N7 O8 S
Name5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163068
DrugBankDB03355
ZINCZINC000015524571
PDB chain4yye Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yye The crystal structure of yeast mitochondrial ThrRS in complex with the canonical threonine tRNA.
Resolution2.301 Å
Binding residue
(original residue number in PDB)		M131 R162 E164 T173 L175 F178 Q180 D182 H184 Q287 V288 Q292 H319 S325 R328
Binding residue
(residue number reindexed from 1)		M96 R127 E129 T138 L140 F143 Q145 D147 H149 Q243 V244 Q248 H275 S281 R284
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C133 R162 Q180 D182 H184 K273 H319
Catalytic site (residue number reindexed from 1) C98 R127 Q145 D147 H149 K229 H275
Enzyme Commision number 6.1.1.3: threonine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004829 threonine-tRNA ligase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0140101 catalytic activity, acting on a tRNA
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006435 threonyl-tRNA aminoacylation
GO:0070159 mitochondrial threonyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yye, PDBe:4yye, PDBj:4yye
PDBsum4yye
PubMed26704982
UniProtP07236|SYTM_YEAST Threonine--tRNA ligase, mitochondrial (Gene Name=MST1)

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