Structure of PDB 5e81 Chain J8 Binding Site BS01

Receptor Information

>5e81 Chain J8 (length=94) Species: 300852 (Thermus thermophilus HB8)

SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRV
RVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELL

Ligand information

>5e81 Chain 1H (length=2885)

aagaugguaagggcccacgguggaugccucggcacccgagccgaugaagg
acguggcuaccugcgauaagccagggggagccgguagcgggcguggaucc
cuggauguccgaaugggggaacccggccggcgggaacgccggucaccgcg
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgcaaacgggggccgaaaaguccgcggcc
guggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggug
agacccaguggaggcccgaaccggugggggaugcaaaccccucggaugag
cuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucucc
ccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagagc
acugauagggcuaggggccuccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggauguuggcuuagaagcagcc
aucauuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaucggggcuuaagcccagcgccgaagcugcgggucugggggauga
ccccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcga
gggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
gggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaac
ccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgc
cuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaa
auccgccggagagcgcaaggguagaagggggccugacugcgaggccugca
agccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugg
aagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugau
cucccccgagcguccacagcggcggggagguuuggcaccucgaugucggc
ucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccc
auuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgguc
ucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacga
gaggaccggaagggacgcaccucugguuucccagcugucccuccaggggc
auaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaag
cgggaagcccgccccaagaugaggccucccacggcgucaagccgguaagg
acccgggaagaccacccgguggaugggccggggguguaagcgccgcgagg
cguugagccgaccggucccaaucguccgaggucuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5e81 Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): S2 K3 K10 R11 I13 V14 A15 N16 R20 R21 A24 K25 R26 G28 G29 V30 G31 K33 T34 T35 K39 R40 R41 Q42 Y43 P44 N45 Q47 R50 R52 R61 S65 K69 L82 K88 L94
• Binding residue (residue number reindexed from 1): S1 K2 K9 R10 I12 V13 A14 N15 R19 R20 A23 K24 R25 G27 G28 V29 G30 K32 T33 T34 K38 R39 R40 Q41 Y42 P43 N44 Q46 R49 R51 R60 S64 K68 L81 K87 L93

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5e81, PDBe:5e81, PDBj:5e81
• PDBsum: 5e81
• PubMed: 26791911
• UniProt: P60494|RL28_THET8 Large ribosomal subunit protein bL28 (Gene Name=rpmB)