Structure of PDB 5el4 Chain 58 Binding Site BS01

Receptor Information

>5el4 Chain 58 (length=138) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>5el4 Chain 1H (length=2833)

aagaugguaagggcccacgguggaugccucggcacccgagccgaugaagg
acguggcuaccugcgauaagccagggggagccgguagcgggcguggaucc
cuggauguccgaaugggggaacccggccggcgggaacgccggucaccgcg
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgcaaacgggggccgaaaaguccgcggcc
guggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggug
agacccaguggaggcccgaaccggugggggaugcaaaccccucggaugag
cuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucucc
ccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagagc
acugauagggcuaggggccuccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacc
ccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagg
gcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaaga
gggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucg
ucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccga
agggcagccgguuaauauuccggcccuucccgcaggugcgauggggggac
gcucuaggcuagggggaccggagccauggacgagcccggccagaagcgca
gggugggagguaggcaaauccgccucccaacaagcucugcguggugggga
agcccguacgggugacaaccccccgaagccagggagccaagaaaagccuc
uaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcggg
ugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaa
guuggccccguaacuucgggagaaggggugcucccuggggugaugagccc
cggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagc
ucucugcgaacucguaagaggagguauagggagcgacgcuugcccggugc
cggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgag
ggacccggugaaauugaacuggccgugaagaugcggccuacccguggcag
gacgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggu
cgcgccugcguaggauaggugggagccugugaacccccgccuccgggugg
gggggaggcgccggugaaauaccacccuggcgcggcugggggccuaaccc
ucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccu
ccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaau
ccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaag
ccgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagcguccacagcggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccucccacggcgucaagccgguaaggac
ccgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcg
uugagccgaccggucccaaucguccgaggucuu

.<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<
<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>
>>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<
<.....>>>>>>.>>...<<<<<<.....<......>......>>>>>.>
.........<<....>>...<<<<<.....<<.....>>....>>>>>..
.<<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<
<...<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<..
...))>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<
<<<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>
......>>.>>>>>>.>>...............<<....>>....>>...
......<<<<....>>>>..................>>>>>>>>>>>...
....<<<<<<<<<<<....>>>>>>>>>>>...<............>.<<
<<<<....<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<
<....>>..<<<<.....>>>>..................>>>>>>>>>>
>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<...
...>>>>>>.....>>>...<<<..<<<<........>>>>.>>>....>
>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<
<<....<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<.
..<<<<<<<<.<...........>.>>>>>>>>..>>.>...>>>>>>>>
>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<
<<......>>>...<<<<.<<<...<<<(((.....<<<<<<........
...<<..<<<<<<<<<..................>>>>>>>>>.>>....
......)))......>>>>>>.>>>...>>>>>>><<<<<<<<.....>>
>>>>>>....>>>>>><.<<<<<...<<<......<<<<<.<<<....>>
>>>>>>...>>>..>>>>>..>.....>>>>>><......<<.....<<<
<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<....
.>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>..
.>>...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....
<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<<...<<<<<
<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>>..>>>...
.<<<......>>>......>>>>>...>>>..>>>>>.........>>>>
...>>...>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<
<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<.........<.
....<<<<<...............>>>>><<<<<<<<<<<<.....>>>>
>>>>>>>>............<<<<<<<<<..<<<.........>>>..<<
<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<
<<<..<<<...<<...<<<<<....>>>>>...>>...>>>>>>>>..>>
>>><<<<<<.......>>>>>>........<...........<<<<<<..
...>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>
>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.<
<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<.<<<
<<<<<<...........<<<.<<..<<......<<<<<<<......>>>>
>>>...>>.............>>>>>..>>>>>>>>>.>>>>>>...<<<
<<....>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<
<<...........>>>>>>..<<...<<<<<<<...<<<<<<.......>
>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<......>
>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<<..))))..
>>>>>>>>>.............>>>>..>>>>>>.......<<<<...<<
<<<<<..<<.......>>>..>>>>>>....>>>.>.......<<<<<.<
<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>.
....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>......
..>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<..........
.....>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>.
..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>>>>
>....>>>.>>>>.......>>>>>>>.....<.....>.......<<<<
<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>
>...>>>..>>>>>.>>>...>>>>....>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5el4 Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
• Resolution: 3.15 Å
• Binding residue (original residue number in PDB): T3 L23 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 R74 Y75 S76 Y78 P79 G80 L82 K83 H94 R97 E100 H101 A102 G105 M106 P111 L112 R114 K118 Q131
• Binding residue (residue number reindexed from 1): T3 L23 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 R74 Y75 S76 Y78 P79 G80 L82 K83 H94 R97 E100 H101 A102 G105 M106 P111 L112 R114 K118 Q131

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5el4, PDBe:5el4, PDBj:5el4
• PDBsum: 5el4
• PubMed: 26791911
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)