Structure of PDB 6th6 Chain Bl Binding Site BS01

Receptor Information
>6th6 Chain Bl (length=93) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYPKQIRTYCPFCKRHTIHKVEKVKKRPRSELSAGQRRFRRKLKGYTGF
PRPNPAGREKPVKKLDLRFRCTVCGKAHTRGQGFRVKKFELVE
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)
M1 P4 R8 H17 R28 S31 L33 R38 R39 R42 K43 G46 Y47 G49 F50 R52 P53 N54 R58 E59 K60 K63 K64 D66 R68 K76 A77 R80 R85
Binding residue
(residue number reindexed from 1)
M1 P4 R8 H17 R28 S31 L33 R38 R39 R42 K43 G46 Y47 G49 F50 R52 P53 N54 R58 E59 K60 K63 K64 D66 R68 K76 A77 R80 R85
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008270 zinc ion binding
GO:0019843 rRNA binding
GO:0046872 metal ion binding
GO:0070180 large ribosomal subunit rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6th6, PDBe:6th6, PDBj:6th6
PDBsum6th6
PubMed32555463
UniProtQ5JE51

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