Structure of PDB 7f6w Chain A Binding Site BS01

Receptor Information
>7f6w Chain A (length=506) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPSQYFETRSRQIQELRKTHEPNPYPHKFHVSISNPEFLAKYAHLKKGET
LPEEKVSIAGRIHAKRESGSKLKFYVLHGDGVEVQLMSQLQDYCDPDSYE
KDHDLLKRGDIVGVEGYVGRTQPKKGGEGEVSVFVSRVQLLTPCLHMLPA
FKDQETRYRKRYLDLIMNKDARNRFITRSEIIRYIRRFLDQRKFIEVETP
MMNVIAGGATAKPFITHHNDLDMDMYMRIAPELFLKQLVVGGLDRVYEIG
RQFRNEGIDMTHNPEFTTCEFYQAYADVYDLMDMTELMFSEMVKEITGSY
IIKYHPDPADPAKELELNFSRPWKRINMIEELEKVFNVKFPSGDQLHTAE
TGEFLKKILVDNKLECPPPLTNARMLDKLVGELEDTCINPTFIFGHPQMM
SPLAKYSRDQPGLCERFEVFVATKEICNAYTELNDPFDQRARFEEQARQK
DQGDDEAQLVDETFCNALEYGLPPTGGWGCGIDRLAMFLTDSNTIREVLL
FPTLKP
Ligand information
Ligand IDKAA
InChIInChI=1S/C16H26N8O7S/c17-4-2-1-3-8(18)15(27)23-32(28,29)30-5-9-11(25)12(26)16(31-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,16,25-26H,1-5,17-18H2,(H,23,27)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1
InChIKeyNARKTLKJPPMFJF-LEJQEAHTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCCCN)N)O)O)N
CACTVS 3.341NCCCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341NCCCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CCCCN
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCCCN)N)O)O)N
FormulaC16 H26 N8 O7 S
Name5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE;
5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE
ChEMBLCHEMBL1163083
DrugBank
ZINCZINC000040956727
PDB chain7f6w Chain A Residue 601 [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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PDB7f6w Human lysyl-tRNA synthetase evolves a dynamic structure that can be stabilized by forming complex.
Resolution2.607 Å
Binding residue
(original residue number in PDB)		E304 R326 H334 N335 F338 E342 E497 I498 N500 Y502 E504 G549 G553 R556
Binding residue
(residue number reindexed from 1)		E232 R254 H262 N263 F266 E270 E425 I426 N428 Y430 E432 G477 G481 R484
Annotation score2
Enzymatic activity
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-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:7f6w, PDBe:7f6w, PDBj:7f6w
PDBsum7f6w
PubMed35133502
UniProtP15180|SYKC_YEAST Lysine--tRNA ligase, cytoplasmic (Gene Name=KRS1)

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