Structure of PDB 1nyr Chain A Binding Site BS03

Receptor Information
>1nyr Chain A (length=642) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
INIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPL
ETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGG
FYYDFDIDQNISSDDFEQIEKTMKQIVNENMKIERKVVSRDEAKELFSND
EYKLELIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGA
YWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEERKERDHRKIGKELELF
TNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDL
YKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYREL
PIRIAELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVV
NMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADE
LGLSYEEAIGEAAFYGPKLDVQVKTAMGKEETLSTAQLDFLLPERFDLTY
IGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPV
NVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQIVV
GDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(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)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain1nyr Chain A Residue 1003 [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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PDB1nyr Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R365 E367 R377 V378 M381 T485 L486 T523 R526
Binding residue
(residue number reindexed from 1)		R362 E364 R374 V375 M378 T482 L483 T520 R523
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C336 R365 L383 D385 H387 K471 H517
Catalytic site (residue number reindexed from 1) C333 R362 L380 D382 H384 K468 H514
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:1nyr, PDBe:1nyr, PDBj:1nyr
PDBsum1nyr
PubMed12875846
UniProtQ8NW68|SYT_STAAW Threonine--tRNA ligase (Gene Name=thrS)

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