Structure of PDB 5vl1 Chain D Binding Site BS01

Receptor Information
>5vl1 Chain D (length=483) Species: 362242 (Mycobacterium ulcerans Agy99) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIPEQFRIRRDKRARLLAEGYDPYPVAIERTHTLAEIRATYADLPTDSAT
EDIVGVAGRVVFARNTGKLCFATLQDGDGTQLQAMISLDEVGRESLDRWK
ADVDIGDVVYVHGTVISSRRGELSVLADSWRMAAKALRPLPVKEMSEESR
VRQRYVDLIVRPQAREVARQRIAVIRAVRNALERRGFLEVETPMLQTLAG
GAAARPFVTHSNALDIDLYLRIAPELFLKRCIVGGFDRVFELNRVFRNEG
SDSTHSPEFSMLETYQTYGTYDDSALITRELIQEVADEAIGTRQLSMPDG
SVYDIDGEWATMEMYSSLSEALGEQITPETTVARLRDIASGLDVESVFGH
GKLVEELWEHAVGNKLTAPTFVKDFPVETTPLTRQHRSIPGVTEKWDLYV
RGVELATGYSELNDPVVQRDRFADQARAAAAGDDEAMQLDEDFLTALEYG
MPPCTGTGMGIDRLLMCLTGLSIRETVLFPIVR
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 chain5vl1 Chain D Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vl1 Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine
Resolution2.7 Å
Binding residue
(original residue number in PDB)		E233 E271 Y273 Y420 E422 G467 G469
Binding residue
(residue number reindexed from 1)		E225 E263 Y265 Y409 E411 G456 G458
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R255 E257 T262 H263 E415 T418 R474
Catalytic site (residue number reindexed from 1) R247 E249 T254 H255 E404 T407 R463
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:0005524 ATP binding
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vl1, PDBe:5vl1, PDBj:5vl1
PDBsum5vl1
PubMed
UniProtA0PV47

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