Structure of PDB 8i1w Chain B Binding Site BS01

Receptor Information
>8i1w Chain B (length=333) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPIVFSGAQPSGELTIGNYMGALRQWVNMQDDYHCIYCIVDQHAITVRQ
DAQKLRKATLDTLALYLACGIDPEKSTIFVQSHVPEHAQLGWALNCYTYF
GELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNLVPVGEDQK
QHLELSRDIAQRFNALYGEIFKVPEPFIPKSGARVMSLLEPTKKMSKSDD
NRNNVIGLLEDPKSVVKKIKRAVTDSDEPPVVRYDVQNKAGVSNLLDILS
AVTGQSIPELEKQFEGKMYGHLKGEVADAVSGMLTELQERYHRFRNDEAF
LQQVMKDGAEKASAHASRTLKAVYEAIGFVAKR
Ligand information
Ligand IDTYM
InChIInChI=1S/C21H24N7O8P/c22-12(5-10-6-24-13-4-2-1-3-11(10)13)21(31)36-37(32,33)34-7-14-16(29)17(30)20(35-14)28-9-27-15-18(23)25-8-26-19(15)28/h1-4,6,8-9,12,14,16-17,20,24,29-30H,5,7,22H2,(H,32,33)(H2,23,25,26)/t12-,14+,16+,17+,20+/m0/s1
InChIKeyIFQVDHDRFCKAAW-SQIXAUHQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](Cc1c[nH]c2ccccc12)C(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)CC(C(=O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N
ACDLabs 10.04O=C(OP(=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)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N
CACTVS 3.341N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
FormulaC21 H24 N7 O8 P
NameTRYPTOPHANYL-5'AMP
ChEMBL
DrugBankDB01831
ZINCZINC000016051386
PDB chain8i1w Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8i1w An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		F7 S8 G9 A10 Q11 G19 N20 G23 A24 V42 Y128 M132 I136 V144 V146 G147 D149 Q150 A184 R185 V186 K195 M196 K198
Binding residue
(residue number reindexed from 1)		F6 S7 G8 A9 Q10 G18 N19 G22 A23 V41 Y127 M131 I135 V143 V145 G146 D148 Q149 A183 R184 V185 K194 M195 K197
Annotation score2
Enzymatic activity
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
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8i1w, PDBe:8i1w, PDBj:8i1w
PDBsum8i1w
PubMed37070195
UniProtP00954|SYW_ECOLI Tryptophan--tRNA ligase (Gene Name=trpS)

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