BioLiP

Receptor Information

>3e9h Chain A (length=484) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ELNDQLRVRREKLKKIEELGVDPFGKRFERTHKAEELFELYGDLSKEELE
EQQIEVAVAGRIMTKRGMGKAGFAHIQDVTGQIQIYVRQDDVGEQQYELF
KISDLGDIVGVRGTMFKTKVGELSIKVSSYEFLTKALRPLPEKDIEQRYR
QRYLDLIMNPESKKTFITRSLIIQSMRRYLDSHGYLEVETPMMHAVAGGA
AARPFITHHNALDMTLYMRIAIELHLKRLIVGGLEKVYEIGRVFRNEGIS
TRHNPEFTMLELYEAYADFRDIMKLTENLIAHIATEVLGTTKIQYGEHLV
DLTPEWRRLHMVDAIKEYVGVDFWRQMSDEEARELAKEHGVEVAPHMTFG
HIVNEFFEQKVEDKLIQPTFIYGHPVEISPLAKKNPDDPRFTDRFELFIV
GREHANAFTELNDPIDQRQRFEEQLKEREQGNDEAHEMDEDFLEALEYGM
PPTGGLGIGVDRLVMLLTNSPSIRDVLLFPQMRH

Ligand ID

KAA

InChI

InChI=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

InChIKey

NARKTLKJPPMFJF-LEJQEAHTSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	NCCCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341	NCCCC[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 10.04	O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CCCCN
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCCCN)N)O)O)N

Formula

C16 H26 N8 O7 S

Name

5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE;
5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE

PDB chain

3e9h Chain A Residue 2002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3e9h Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate
Resolution	2.1 Å
Binding residue (original residue number in PDB)	E231 R253 H261 N262 F265 M267 E269 Y271 E411 H412 N414 F416 E418 G463 G467 R470
Binding residue (residue number reindexed from 1)	E223 R245 H253 N254 F257 M259 E261 Y263 E403 H404 N406 F408 E410 G455 G459 R462
Annotation score	2
Binding affinity	PDBbind-CN: -logKd/Ki=7.55,Ki=28nM

Catalytic site (original residue number in PDB)	R253 E255 R260 H261 E411 N414 R470
Catalytic site (residue number reindexed from 1)	R245 E247 R252 H253 E403 N406 R462
Enzyme Commision number	6.1.1.6: lysine--tRNA ligase.

	Molecular Function
GO:0000049	tRNA binding
GO:0000166	nucleotide binding
GO:0000287	magnesium ion binding
GO:0003676	nucleic acid binding
GO:0004812	aminoacyl-tRNA ligase activity
GO:0004824	lysine-tRNA ligase activity
GO:0005524	ATP binding
GO:0016740	transferase activity
GO:0046872	metal ion binding

	Biological Process
GO:0006412	translation
GO:0006418	tRNA aminoacylation for protein translation
GO:0006430	lysyl-tRNA aminoacylation

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol

PDB	RCSB:3e9h, PDBe:3e9h, PDBj:3e9h
PDBsum	3e9h
PubMed	19174549
UniProt	Q9RHV9\|SYK_GEOSE Lysine--tRNA ligase (Gene Name=lysS)

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Structure of PDB 3e9h Chain A Binding Site BS02