Structure of PDB 5on3 Chain D Binding Site BS01

Receptor Information
>5on3 Chain D (length=850) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHM
GHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPW
TYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVY
KKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYAD
ELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRP
DAFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTEKKGVDTGFKAV
HPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVI
LAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGE
RKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVM
DGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYYARYTCPQYKE
GMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPA
KQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGH
ELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQE
SGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKALRRDVHKTIA
KVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLAVVRM
LNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDSTLVVVQVNGKV
RAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYVPGKLLNLVVG
Ligand information
>5on3 Chain E (length=79) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gcccggaugguggaaucgguagacacaagggauucccucggcgcgcgcug
ugcggguucaagucccgcuccggguacca
<<<<<<<..<<<...........>>>.<<<<<.>>>>>.<<<<..>>>>.
.<<<<<.......>>>>>>>>>>>>....
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5on3 Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D80 G83 L84 A167 N168 E169 T215 M219 N222 W223 R416 L417 R418 R424 F493 E532 H533 M536 M617 S618 K619 F648 A649 P651 Q659 G665 R668 K675 K711 R719 N723 T724 M730 E731 N734 L801 V803 R811 K813 K846 V850 N856
Binding residue
(residue number reindexed from 1)		D80 G83 L84 A167 N168 E169 T215 M219 N222 W223 R406 L407 R408 R414 F483 E522 H523 M526 M607 S608 K609 F638 A639 P641 Q649 G655 R658 K665 K701 R709 N713 T714 M720 E721 N724 L791 V793 R801 K803 K836 V840 N846
Enzymatic activity
Catalytic site (original residue number in PDB) F493 H533 F543 K619 K622
Catalytic site (residue number reindexed from 1) F483 H523 F533 K609 K612
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:0004823 leucine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
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:5on3, PDBe:5on3, PDBj:5on3
PDBsum5on3
PubMed29111343
UniProtP07813|SYL_ECOLI Leucine--tRNA ligase (Gene Name=leuS)

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