Structure of PDB 5y0q Chain B Binding Site BS01

Receptor Information
>5y0q Chain B (length=401) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKAVGLVVEYNPFHNGHLYHAQTAKLQTGCDTAVAVMSGHFLQRGEPAVV
SKWARTKMALQSGVDLVIELPYLYAVQKADIFARGSVSILNELECEALFF
GSENGDIKPFLETAQLIDEHKHILNDRIKEELKKGASYPAAAAIAFSSIL
HTESALDLSKPNNILGYQYVTSILTGGYPMKPYTTARINHIASATSIRKA
MIGQNLEACLRFLPAASARELAAYRKSFGLWHTPESYFSYLKYSLSTVTA
RELQQVYEVEEGLEHRIIRSIRKSSSYQEFMELLKTKRYTWTRLQRMNTH
ILTRTKKQDMQKLLDNDKAPYIRLLGMTKKGQAYLSEKKKALSVPLVSKL
SSFSHPALDLDVKASRIYSLPIEEPLRTEFDLQEYGHAPIRYDEDEQHFL
N
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain5y0q Chain B Residue 1001 [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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PDB5y0q Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E9 H14 G16 H17 R44 G101 A186 R187 S206
Binding residue
(residue number reindexed from 1)		E9 H14 G16 H17 R44 G101 A186 R187 S193
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.4.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016879 ligase activity, forming carbon-nitrogen bonds
Biological Process
GO:0006400 tRNA modification
GO:0008033 tRNA processing
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:5y0q, PDBe:5y0q, PDBj:5y0q
PDBsum5y0q
PubMed30150682
UniProtO34513|TMCAL_BACSU tRNA(Met) cytidine acetate ligase (Gene Name=tmcAL)

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