Structure of PDB 5dk4 Chain A Binding Site BS01

Receptor Information
>5dk4 Chain A (length=328) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQ
DPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYI
GELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQ
HIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPN
PKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLS
GQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRV
LDEGAEKANRVASEMVRKMEQAMGLGRR
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 chain5dk4 Chain A Residue 401 [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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PDB5dk4 Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I8 Q9 S11 G17 N18 G21 V143 G144 D146 A181 I183 K192 M193 S194 K195 S196
Binding residue
(residue number reindexed from 1)		I9 Q10 S12 G18 N19 G22 V144 G145 D147 A182 I184 K193 M194 S195 K196 S197
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K111 K192 K195
Catalytic site (residue number reindexed from 1) K112 K193 K196
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:5dk4, PDBe:5dk4, PDBj:5dk4
PDBsum5dk4
PubMed26555258
UniProtP00953|SYW_GEOSE Tryptophan--tRNA ligase (Gene Name=trpS)

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