Structure of PDB 1vbm Chain B Binding Site BS01

Receptor Information
>1vbm Chain B (length=318) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLIKQLQERGLVAQVTDEEALAERLAQGPIALYCGFDPTADSLHLGHLVP
LLCLKRFQQAGHKPVALVGGATGLIGDPSFKAAERKLNTEETVQEWVDKI
RKQVAPFLDFDCGENSAIAANNYDWFGNMNVLTFLRDIGKHFSVNQMINK
EAVKQRLNREDQGISFTEFSYNLLQGYDFACLNKQYGVVLQIGGSDQWGN
ITSGIDLTRRLHQNQVFGLTVPLITKADGTKFGKTEGGAVWLDPKKTSPY
KFYQFWINTADADVYRFLKFFTFMSIEEINALEEEDKNSGKAPRAQYVLA
EQVTRLVHGEEGLQAAKR
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 chain1vbm Chain B Residue 3002 [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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PDB1vbm Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y37 G39 D41 G50 H51 V53 P54 D81 Y175 Q179 D182 G198 D200 Q201 L227 I228
Binding residue
(residue number reindexed from 1)		Y33 G35 D37 G46 H47 V49 P50 D77 Y171 Q175 D178 G194 D196 Q197 L223 I224
Annotation score2
Binding affinityBindingDB: Ki=2.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) T43 H48 H51 K85 R89 Q179 D200 K235 K238 T239
Catalytic site (residue number reindexed from 1) T39 H44 H47 K81 R85 Q175 D196 K231 K234 T235
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:1vbm, PDBe:1vbm, PDBj:1vbm
PDBsum1vbm
PubMed15663931
UniProtP0AGJ9|SYY_ECOLI Tyrosine--tRNA ligase (Gene Name=tyrS)

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