Structure of PDB 6kid Chain A Binding Site BS02

Receptor Information
>6kid Chain A (length=1004) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TAKVDFLKKIEKEIQQKWDTERVFEVNASNLEKQTSKGKYFVTFPYPYMN
GRLHLGHTFSLSKCEFAVGYQRLKGKCCLFPFGLHCTGMPIKACADKLKR
EIELYGCPPDFPSKYQWGIMKSLGLSDEEIVKFSEAEHWLDYFPPLAIQD
LKRMGLKVDWRRSFITTDVNPYYDSFVRWQFLTLRERNKIKFGKRYTIYS
PKDGQPCMDHDRQTGEGVGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVA
ATLRPETMFGQTNCWVRPDMKYIGFETVNGDIFICTQKAARNMSYQGFTK
DNGVVPVVKELMGEEILGASLSAPLTSYKVIYVLPMLTIKEDKGTGVVTS
VPSDSPDDIAALRDLKKKQALRAKYGIRDDMVLPFEPVPVIEIPGFGNLS
AVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGIMLVDGFKGQKVQDVK
KTIQKKMIDAGDALIYMEPEKQVMSRSSDECVVALCDQWYLDYGEENWKK
QTSQCLKNLETFCEETRRNFEATLGWLQEHACSRTYGLGTHLPWDEQWLI
ESLSDSTIYMAFYTVAHLLQGGNLHGQAESPLGIRPQQMTKEVWDYVFFK
EAPFPKTQIAKEKLDQLKQEFEFWYPVDLRVSGKDLVPNHLSYYLYNHVA
MWPEQSDKWPTAVRANGHLLLNSEKMSKSTGNFLTLTQAIDKFSADGMRL
ALADAGDTVEDANFVEAMADAGILRLYTWVEWVKEMVANWDSLRSGPAST
FNDRVFASELNAGIIKTDQNYEKMMFKEALKTGFFEFQAAKDKYRELAVE
GMHRELVFRFIEVQTLLLAPFCPHLCEHIWTLLGKPDSIMNASWPVAGPV
NEVLIHSSQYLMEVTHDLRLRLKNYPSHCTIYVAKNYPPWQHTTLSVLRK
HFEANNGKLPDNKVIASELGSMPELKKYMKKVMPFVAMIKENLEKMGPRI
LDLQLEFDEKAVLMENIVYLTNSLELEHIEVKFASEAEDKIREDCCPGKP
LNVF
Ligand information
Ligand IDLEU
InChIInChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1
InChIKeyROHFNLRQFUQHCH-YFKPBYRVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C[C@@H](C(=O)O)N
CACTVS 3.341CC(C)C[C@H](N)C(O)=O
OpenEye OEToolkits 1.5.0CC(C)CC(C(=O)O)N
ACDLabs 10.04O=C(O)C(N)CC(C)C
CACTVS 3.341CC(C)C[CH](N)C(O)=O
FormulaC6 H13 N O2
NameLEUCINE
ChEMBLCHEMBL291962
DrugBankDB00149
ZINCZINC000003645145
PDB chain6kid Chain A Residue 1202 [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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PDB6kid Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		T293 T390 S396 D399 Y468
Binding residue
(residue number reindexed from 1)		T252 T349 S355 D358 Y427
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004819 glutamine-tRNA ligase activity
GO:0004823 leucine-tRNA ligase activity
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006425 glutaminyl-tRNA aminoacylation
GO:0006429 leucyl-tRNA aminoacylation
GO:0008361 regulation of cell size
GO:0032008 positive regulation of TOR signaling
GO:0034198 cellular response to amino acid starvation
GO:0043547 positive regulation of GTPase activity
GO:0071230 cellular response to amino acid stimulus
GO:0071233 cellular response to L-leucine
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
GO:1904263 positive regulation of TORC1 signaling
GO:1990253 cellular response to leucine starvation
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0012505 endomembrane system
GO:0016604 nuclear body
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6kid, PDBe:6kid, PDBj:6kid
PDBsum6kid
PubMed33910001
UniProtQ9P2J5|SYLC_HUMAN Leucine--tRNA ligase, cytoplasmic (Gene Name=LARS1)

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