Structure of PDB 2pid Chain A Binding Site BS01

Receptor Information
>2pid Chain A (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLLAAQKARGLFKDFFPETGTKIELPELFPQTIYCGFDPTADSLHVGHLL
ALLGLFHLQRAGHNVIALVGGATARLGDPSGRTKEREALETERVRANARA
LRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQHLVDFLAAVGGHF
RMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRVQLG
GSDQLGNIMSGYEFINKLTGEDVFGITVPLITAVWLNRDKTSPFELYQFF
VRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKL
VHGREGLDSAKRCTQAL
Ligand information
Ligand IDYSA
InChIInChI=1S/C19H23N7O8S/c20-11(5-9-1-3-10(27)4-2-9)18(30)25-35(31,32)33-6-12-14(28)15(29)19(34-12)26-8-24-13-16(21)22-7-23-17(13)26/h1-4,7-8,11-12,14-15,19,27-29H,5-6,20H2,(H,25,30)(H2,21,22,23)/t11-,12+,14+,15+,19+/m0/s1
InChIKeyMJZAZMKENKZBAJ-QTOWJTHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)N)O
CACTVS 3.341N[CH](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34
CACTVS 3.341N[C@@H](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
OpenEye OEToolkits 1.5.0c1cc(ccc1CC(C(=O)NS(=O)(=O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)N)O
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc4ccc(O)cc4
FormulaC19 H23 N7 O8 S
Name5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE;
TYROSYLADENYLATE
ChEMBLCHEMBL1163085
DrugBankDB03325
ZINCZINC000016052371
PDB chain2pid Chain A Residue 384 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2pid Crystal Structure of Human Mitochondrial Tyrosyl-tRNA Synthetase Reveals Common and Idiosyncratic Features.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y77 G79 D81 G90 H91 Y221 Q225 D228 G243 G244 D246 Q247 L273 I274
Binding residue
(residue number reindexed from 1)		Y34 G36 D38 G47 H48 Y178 Q182 D185 G200 G201 D203 Q204 L230 I231
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T83 H88 H91 R125 R129 Q225 D246
Catalytic site (residue number reindexed from 1) T40 H45 H48 R82 R86 Q182 D203
Enzyme Commision number 6.1.1.1: tyrosine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004831 tyrosine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006437 tyrosyl-tRNA aminoacylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2pid, PDBe:2pid, PDBj:2pid
PDBsum2pid
PubMed17997975
UniProtQ9Y2Z4|SYYM_HUMAN Tyrosine--tRNA ligase, mitochondrial (Gene Name=YARS2)

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