Structure of PDB 4eo4 Chain D Binding Site BS01

Receptor Information
>4eo4 Chain D (length=414) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATMTSMVSQRQDLFMTDPLSPGSMFFLPNGAKIFNKLIEFMKLQQKFKFG
FNEVVTPLIYKKTLWEKSGHWENYADDMFKVETKEEYGLKPMNCPGHCLI
FGKKDRSYNELPLRFSDFSPLHRNEASGALSGLTRLRKFHQDDGHIFCTP
SQVKSEIFNSLKLIDIVYNKIFPSNYFINFSTRPDHFIGDLKVWNHAEQV
LKEILEESGKPWKLNPGDGAFYGPKLDIMVTDHLRKTHQVATIQLDFQLP
ERFDLKFKDQDNSYKRPIMIHRATFGSIERFMALLIDSNEGRWPFWLNPY
QAVIIPVNTKNVQQLDMCTALQKKLRNELEADDMEPVPLNDWHFNVDLDI
RNEPVGYRIKSAILKNYSYLIIVGDEEVQLQKYNIRERDNRKSFEKLTMS
QIWEKFIELEKNYK
Ligand information
Ligand IDSSA
InChIInChI=1S/C13H19N7O8S/c14-5(1-21)12(24)19-29(25,26)27-2-6-8(22)9(23)13(28-6)20-4-18-7-10(15)16-3-17-11(7)20/h3-6,8-9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,8+,9+,13+/m0/s1
InChIKeyHQXFJGONGJPTLZ-YTMOPEAISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O)N
CACTVS 3.341N[CH](CO)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CO)N)O)O)N
FormulaC13 H19 N7 O8 S
Name5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163070
DrugBankDB03869
ZINCZINC000013542770
PDB chain4eo4 Chain D Residue 1001 [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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PDB4eo4 The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase.
Resolution2.87 Å
Binding residue
(original residue number in PDB)		M131 C133 R162 E164 T173 L175 F178 Q180 D182 Q287 V288 Q292 G324 S325 R328
Binding residue
(residue number reindexed from 1)		M92 C94 R123 E125 T134 L136 F139 Q141 D143 Q239 V240 Q244 G276 S277 R280
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) C94 R123 Q141 D143 H145 K225 H271
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:4eo4, PDBe:4eo4, PDBj:4eo4
PDBsum4eo4
PubMed22773845
UniProtP07236|SYTM_YEAST Threonine--tRNA ligase, mitochondrial (Gene Name=MST1)

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