Structure of PDB 1nyr Chain B Binding Site BS02

Receptor Information
>1nyr Chain B (length=637) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLT
KPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVI
EGGFYYDFDIDQNISSDDFEQIEKTMKQIVNENMKIERKVVSRDEAKELE
LIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGD
SNNKMLQRIYGTAFFDKKELKAHLQMLEERKERDHRKIGKELELFTNSQL
VGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSG
HWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRIA
ELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIID
VYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSY
EEAIGEAAFYGPKLDVQVKTAMGKEETLSTAQLDFLLPERFDLTYIGQDG
EHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLH
YDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQIVVGDKEV
ENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR
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 B Residue 2003 [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 R377 V378 M381 S522 T523 R526
Binding residue
(residue number reindexed from 1)		R357 R369 V370 M373 S514 T515 R518
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) C328 R357 L375 D377 H379 K463 H509
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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