Structure of PDB 6th6 Chain Bj Binding Site BS01

Receptor Information
>6th6 Chain Bj (length=47) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARFPEAEARIFRKLVCMRCGATNPWGAKKCRKCGYKGLRPKAREPRG
Ligand information
>6th6 Chain BA (length=2934) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cccgguggcaacuaagccgccugguggauggcucggcucggggcgccgac
gaagggcguggcaagcugcgauaagccccggcgaggcgcaggcagccguc
gaaccggggaugcccgaaugggaccucccgcggcuugccgcacucccagu
cgggagggggaacgcggggaauugaaacaucuuaguacccgcaggaaaag
aaagcaaaagcgaugccguuaguaggggcgaccgaaagcggcacagggca
aacugaaccccgggccgaaagguucgggggaugugguguuguagggcccg
cggaggagcccugggggcgaagccgaaguccgcuggaacgcggcgccgga
gagggugaaagccccguaggcguaagcccccgagcuccugcggugucccu
gaguaccgucggucggauauccggcgggaagcugggaggcaucggcuccc
aacccuaaauacgucccgagaccgauagcgaacuaguaccgugagggaaa
gcugaaaagcaccccgggaggggggugaaaagagccugaaaccaggcggc
gauaggagggugcggcccgaaaggguugacccuccccgaaggaaacacgg
gcgaccguggaguacgaggggaggugaccgggguugcaccguccgucuug
gaucacggggcagggaguucacccgagcggcgagguuaagggggucaacc
ccgaagccgcagggaaaccgacagguccgcagcccguagggcgagggacg
gggugugaaagcgcccggagucgcucgggugagacccgaagccggucgau
cuagcccggggcagggugaagucccucaacagagggauggaggcccgcua
ggggugcugacgcgcaauucgcucccgugaccccgggcuaggggugaaag
gccaaucgaggccggcgauagcugguucccgccgaauuaucccccaggau
agcccggccggagguaggcagugggguagagcacugauuggggguuuagg
gggcgaaagccuccggcucccugucaaacuccgaacccacugccgccgua
gauggccggaguaggggggcgguguaagccgucacccgagaggggaacaa
cccagaccgggguuaaggccccaaagugccggcuaaguguuacuccaaag
ggugucccuggccuuagacagcggcccgucgaggucaggggccccgaaaa
uggacggggcuuaagccggccgccgagaccccggcgcacggaccgauugg
uccgugaucggguaggcgggcgugccgauggggcggaagccgggccguga
gguccgguggacccgucgguauugcggauccugccgggaguagcagcaua
gccgggugagaaucccggccgccguaggggccaggguuccacggcaaugu
ucgucagccguggguuagucgguccuaacccgacccguaacucggcgucg
gggaaagggaaacggguuuauauucccguaccgcggugguaggugcggca
acgcaagcccgaggggugacgccucgggguaggcggaccgguccacaagg
ccggcuaagcguauaagcccggggagugccguaauggcgagaaccgggug
aaagcgcgaauggccucccguaagggggguuccgccgaucccuggggccc
gugaaaagccccucgggaacgauccaccgcgaccguaccgagaaccgaca
cuggugccccugggugagaagccuaaggcgugucgggggaaacccagccg
agggaacucggcaaauuggccccguaacuucgggagaaggggugccugcg
gguguguaacccgcaggucgcagugacuaggggggcccgacuguuuagua
aaaacacaggucccagcuagcccgaaaggguuuguacuggggccgacgcc
ugcccagugccgguaugugaagcccggguacaaccgggugaagcaccggu
aaacggcggggguaacuauaacccucuuaagguagcgaaauuccuugucg
guuaaaugccgaccugcaugaauggcguaacgagguccccacuguccccg
gcuggggcccggcgaaaccucugccaggcgcauaugccugggaccuccgg
ugggaagcgaagaccccauggagcuuuacugcagccugccguugccguac
ggcggggggugcgcagcguaggcgggaggcgucgaagcccgcccuccggg
gcggguggagccgcccaugagacaccgcccacccucugccguacggcuaa
cccgcggaagcggggacagcgguaggugggcaguuuggcuggggcggcac
acccucgaaaagguaucgagggugcccuaaggucggcucaggcgggucag
gaauccgccguagagugcaagggcaaaagccggccugacuggacccguaa
cagaggcggguccagccgcgaaagcguggccuagcgaaccccugugccuc
cccggugggggccagggaugacagaaaagcuacccuggggauaacagagu
cgucucgggcgagagcccauaucgaccccgaggcuugcuaccucgcuguc
ggcucuucccauccuggcccugcagcaggggccaaggguggggguguuca
cccauuaaaggggaacgugagcuggguuuagaccgucgugagacaggucg
gaugcuaucuaccggagguguuggccgccugaggggaaggcucccccagu
acgagaggaacagggagccgcggccucuggucuaccgguuguccuacagg
gcauagccgggcagcuacgccgcagccgauaaggccugaaagcaucuaag
gccgaagcggcccccgaaaacaggcggccaccgagggcccgggaagaaga
cccgguugauggggcggggauguaagcgggaagggaaaccgacccguuca
gucugccgcucccaacagcccgagugcuaccggg
<.<<<<<<<<.....<<<<<<<<<<.....<<..<<<<<<<.[<<<<...
...<<<<<<.((..((.>>>.....<<<<<<...<<<))..)).>>>...
...>>>>>>...>>>....<<<....>>><<<<<..>>>>>.<<<<<...
.>>>>>.>>....<<<<<.....<......>......>>>>>........
...<<....>>..<<<<<<.....<<.....>>....>>>>>>..<<<..
.<<<...<<<<<<<<<....>>>>>>>>>.....>>>.....<<<<.<<<
<....<<<<..<<<<<<<...<<<.....<<<<......>>>>.((....
..<<<.....))>>>...>>>....>>>>>>>.>>>>..>>>>...>>>>
.....<<<<<<<........>>>>>>>......<<<<<.<<<<<<>>>>>
..>>>......>>.]>>>>>.>>...............<<....>>....
>>.........<<<<....>>>>.................>>>>>>>>>>
........<<<<<<<<<<....<<....<.<<<<<<<...<....<<<<<
....>>>>>.....>..>>>>>>>>..>>.>>>>>>>>>>..<<<<....
....>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<.....>>
>>...>>>...<<....>>.....<<<<...<<<<...>>>>...>>>>.
<<<<<<....>>>>>>...>>>>>>>>>>>>>..<<.<..<<<<<<<...
..<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>....
<<<..<<.<<........>>>>.>>>....>>>>>>>>>...<<<.....
>>>......>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>
><<<<<<<<<..<<<.<<<<<<<<<...<<<...<<<<.<<<<<<....<
<<<.......>>>>.>>>>>>.>>>>..>>.>...>>>>>>>>>>>>...
..>>>>>>>.>>..<<<<<<<<<....>>>>>>.>>>....<<<......
>>>...<<<<<<<...<<<(((.....<<<<<<.....<<.........<
<<.<<<<<<<<<<.........<..>......>>>>>>>>>>>>>.....
.....)))>>....>>>>>>.>>>...>>>>>>><<<<<<<<<<....>>
>>>>>>..>>....>>>>>><<<<<<<<<<<<......<<<<<<<<....
>>>>>>>>...>>>>>>>>>>.>>.....>>>>>><<.....<<......
<<<<<<.......>>>>>><<<<....<<<...<<...<<<<<<...<<.
....>>.>>>>>>....((<<<<<<...<<<<<<<<<.....>>>.>>>>
>>....>>...<<<<<........>>>>>))<<<<<<<<.....<<<...
.>>>...<<<<<<<<<<...<<<<<<<<<..<<<<<<<<<<<<....{>>
>>>>....<<<<.<..<<<<<<.....<<<<...>>>>.....>>>>>>.
..>>>>>.....<<<<<<......>>>>>>>>>>>>...>>>>>>>>>..
.......>>>>>>>>>>......>>>>>>>>>>>>..>>.....<<....
..>>...>>>.<<<<.....>>>>..>>>>...<<<<.....<<<<<<<<
.<<.........<.....<<<<<...............>>>>><<<<<<<
<<<.....>>>>>>>>>>............<<<<<<<<<..<<<......
...>>>..<<<<<<<....<<<<....>>>>......>>>>>>>.<<<<<
.<<<..<<<<<<<..<<<...<<<<<<......>>>>>>...>>>>>>>>
..>>>>><<<<<<.......>>>>>>........<...........<<<<
<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>
>>>>>>.>>>>>>....>>....<<<<<........>>>>>..<<<<<<<
<.<<<.[[......<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<<<<<<
<<<<..<<<<..........<<<<<..<<<......<<<<<<.<<...>>
>>>>>>...>>>............>>>>>.>.>>>.>>>>>>>>>>>...
<<<<<....>>>>>....>>>>>>>>>..>>>>>.....<.....>....
<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<....
...>>>>>>.....<<...(((>>....>>>>>>>...<<<<<<<<<<..
.....>>>>>>>>>>.<<<....>>>.>>))).......<<<<<.<<<<<
.>>>>>>>>>>>>>>>>..........>>>>..]]>>>>.......<<<<
.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<
<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>..<<<.......
>>>......>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>.
...]]..>>>>>>>>>>>....<<<<<<<<..<<<<..<<<<<<<.....
............>>>>>>><<<<<...<<<<...<<<<<<<<<<}...>>
>>>..>>>>>...>>>>.>>>>>.<<<<.<..<<<<<...........>>
>>>...>>>>>>>>>>......>>>>>>>.....<<<<<<<<<.......
>>>>>....<<<<<<<<<<<<....<<<<<..<<....>>..>>>>>...
>>>>.>>>>>.>>>...>>>>...>>>>>>>>.>
Receptor-Ligand Complex Structure
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PDB6th6 Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
Resolution2.55 Å
Binding residue
(original residue number in PDB)
M18 R19 T23 P25 K30 R32 K37 R40 K42 A43 R47 G48
Binding residue
(residue number reindexed from 1)
M17 R18 T22 P24 K29 R31 K36 R39 K41 A42 R46 G47
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6th6, PDBe:6th6, PDBj:6th6
PDBsum6th6
PubMed32555463
UniProtQ5JJD3|RL40_THEKO Large ribosomal subunit protein eL40 (Gene Name=rpl40e)

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