Structure of PDB 1nyq Chain B Binding Site BS02

Receptor Information
>1nyq Chain B (length=645) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLT
KPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVI
EGGFYYDFDIDQNISSDDFEQIEKTMKQIVNENMKIERKVVSRDEAKELF
SNDEYKLELIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLST
AGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEERKERDHRKIGKEL
ELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLAN
VDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSY
RELPIRIAELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFK
RVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEA
ADELGLSYEEAIGEAAFYGPKLDVQVKTAMGKEETLSTAQLDFLLPERFD
LTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQI
IPVNVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQ
IVVGDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR
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 chain1nyq Chain B Residue 2002 [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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PDB1nyq Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase
Resolution3.2 Å
Binding residue
(original residue number in PDB)		M334 C336 R365 E367 Q376 R377 V378 M381 L383 D385 H387 Y468 T485 Q490 H517 T523 R526
Binding residue
(residue number reindexed from 1)		M334 C336 R365 E367 Q376 R377 V378 M381 L383 D385 H387 Y468 T485 Q490 H517 T523 R526
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C336 R365 L383 D385 H387 K471 H517
Catalytic site (residue number reindexed from 1) C336 R365 L383 D385 H387 K471 H517
Enzyme Commision number 6.1.1.3: threonine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004829 threonine-tRNA ligase activity
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006435 threonyl-tRNA aminoacylation
GO:0043039 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:1nyq, PDBe:1nyq, PDBj:1nyq
PDBsum1nyq
PubMed12875846
UniProtQ8NW68|SYT_STAAW Threonine--tRNA ligase (Gene Name=thrS)

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