Structure of PDB 2yy5 Chain D Binding Site BS01

Receptor Information
>2yy5 Chain D (length=346) Species: 272634 (Mycoplasmoides pneumoniae M129) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDF
QPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNL
GELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVP
VGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKK
MSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFASKTQPGVTNML
TILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNI
QRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK
Ligand information
Ligand IDWSA
InChIInChI=1S/C21H24N8O7S/c22-12(5-10-6-24-13-4-2-1-3-11(10)13)20(32)28-37(33,34)35-7-14-16(30)17(31)21(36-14)29-9-27-15-18(23)25-8-26-19(15)29/h1-4,6,8-9,12,14,16-17,21,24,30-31H,5,7,22H2,(H,28,32)(H2,23,25,26)/t12-,14+,16+,17+,21+/m0/s1
InChIKeyRQAVKMXDGHWLGD-BFNSABJLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)CC(C(=O)NS(=O)(=O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc5c4ccccc4nc5
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N
CACTVS 3.341N[CH](Cc1c[nH]c2ccccc12)C(=O)N[S](=O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45
CACTVS 3.341N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[S](=O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
FormulaC21 H24 N8 O7 S
Name5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE
ChEMBLCHEMBL1163060
DrugBank
ZINCZINC000044387166
PDB chain2yy5 Chain D Residue 1353 [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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PDB2yy5 Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae
Resolution2.55 Å
Binding residue
(original residue number in PDB)		T7 G8 Q10 G18 N19 G22 H44 M137 I141 V149 V151 G152 D154 Q155 N189 R190 I191 K200 M201
Binding residue
(residue number reindexed from 1)		T7 G8 Q10 G18 N19 G22 H44 M137 I141 V149 V151 G152 D154 Q155 N189 R190 I191 K200 M201
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K112 K200 K203
Catalytic site (residue number reindexed from 1) K112 K200 K203
Enzyme Commision number 6.1.1.2: tryptophan--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004830 tryptophan-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-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:2yy5, PDBe:2yy5, PDBj:2yy5
PDBsum2yy5
PubMed
UniProtP75510|SYW_MYCPN Tryptophan--tRNA ligase (Gene Name=trpS)

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