Structure of PDB 1bbu Chain A Binding Site BS01

Receptor Information
>1bbu Chain A (length=486) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVDLNNELKTRREKLANLREQGIAFPNDFRRDHTSDQLHAEFDGKENEEL
EALNIEVAVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDDLPEGVYNE
QFKKWDLGDILGAKGKLFKTKTGELSIHCTELRLLTKALRPLPDDQEARY
RQRYLDLISNDESRNTFKVRSQILSGIRQFMVNRGFMEVETPMMQVIPGG
AAARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGI
SVRHNPEFTMMELYMAYADYKDLIELTESLFRTLAQDILGKTEVTYGDVT
LDFGKPFEKLTMREAIKKYRPETDMADLDNFDSAKAIAESIGIHVEKSWG
LGRIVTEIFEEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFF
IGGREIGNGFSELNDAEDQAQRFLDQVAAKDAGDDEAMFYDEDYVTALEH
GLPPTAGLGIGIDRMVMLFTNSHTIRDVILFPAMRP
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain1bbu Chain A Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1bbu Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G216 E240 E278 Y280 F426 E428 G473 G475
Binding residue
(residue number reindexed from 1)		G200 E224 E262 Y264 F410 E412 G457 G459
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R262 E264 R269 H270 E421 N424 R480
Catalytic site (residue number reindexed from 1) R246 E248 R253 H254 E405 N408 R464
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
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:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042803 protein homodimerization 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
GO:0016020 membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1bbu, PDBe:1bbu, PDBj:1bbu
PDBsum1bbu
PubMed11041850
UniProtP0A8N3|SYK1_ECOLI Lysine--tRNA ligase (Gene Name=lysS)

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