Structure of PDB 6skf Chain BG Binding Site BS01

Receptor Information

>6skf Chain BG (length=183) Species: 311400 (Thermococcus kodakarensis)

PVDAWIREEIEIPEGVEVTVEGNTVKVKGPKGELQRELKYPGVQIFTEDG
KVVIYKEFPRKKDVAIVRTFKAHINNMIKGVTEGFKYRLKVVYSHFPMTV
KVQGDEVVIENFLGEKNPRRAKILPGVTVKVKGSEIEVEGIDKEAVGQTA
ANIEQATRITKWDRRVFQDGIYIVEKAGKPIKF

Ligand information

>6skf Chain BA (length=2929)

cccgguggcaacuaagccgccugguggauggcucggcucggggcgccgac
gaagggcguggcaagcugcgauaagccccggcgaggcgcaggcagccguc
gaaccggggaugcccgaaugggaccucccgcggcuugccgcacucccagu
cgggagggggaacgcggggaauugaaacaucuuaguacccgcaggaaaag
aaagcaaaagcgaugccguuaguaggggcgaccgaaagcggcacagggca
aacugaaccccgggccgaaagguucgggggaugugguguuguagggcccg
cggaggagcccugggggcgaagccgaaguccgcuggaacgcggcgccgga
gagggugaaagccccguaggcguaagcccccgagcuccugcggugucccu
gaguaccgucggucggauauccggcgggaagcugggaggcaucggcuccc
aacccuaaauacgucccgagaccgauagcgaacuaguaccgugagggaaa
gcugaaaagcaccccgggaggggggugaaaagagccugaagccaggcggc
gauaggagggugcggcccgaaaggguugacccuccccgaaggaaacacgg
gcgaccguggaguacgaggggaggugaccgggguugcaccguccgucuug
gaucacggggcagggaguucacccgagcggcgagguuaagggggucaacc
ccgaagccgcagggaaaccgacagguccgcagcccguagggcgagggacg
gggugugaaagcgcccggagucgcucgggugagacccgaagccggucgau
cuagcccggggcagggugaagucccucaacagagggauggaggcccgcua
ggggugcugacgugcaauucgcucccgugaccccgggcuaggggugaaag
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
acccucgaaaagguaucgagggugcccuaaggucggcucaggcgggucuc
cgccguagagugcaagggcaaaagccggccugacuggacccguaacagag
gcggguccagccgcgaaagcguggccuagcgaaccccugugccuccccgg
ugggggccagggaugacagaaaagcuacccuggggauaacagagucgucu
cgggcgagagcccauaucgaccccgaggcuugcuaccucgcugucggcuc
uucccauccuggcccugcagcaggggccaaggguggggguguucacccau
uaaaggggaacgugagcuggguuuagaccgucgugagacaggucggaugc
uaucuaccggagguguuggccgccugaggggaaggcucccccaguacgag
aggaacagggagccgcggccucuggucuaccgguuguccuacagggcaua
gccgggcagcuacgccgcagccgauaaggccugaaagcaucuaaggccga
agcggcccccgaaaacaggcggccaccgagggcccgggaagaagacccgg
uugauggggcggggauguaagcgggaagggaaaccgacccguucagucug
ccgcucccaacagcccgagugcuaccggg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6skf Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): R61 K62 K63 A66 T70 A73 F97 E116 K117 N118 K144 E145 G148 Q149 Q156 R159 T161 D164 V167 K177
• Binding residue (residue number reindexed from 1): R60 K61 K62 A65 T69 A72 F96 E115 K116 N117 K143 E144 G147 Q148 Q155 R158 T160 D163 V166 K176

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6skf, PDBe:6skf, PDBj:6skf
• PDBsum: 6skf
• PubMed: 32555463
• UniProt: Q5JJG4|RL6_THEKO Large ribosomal subunit protein uL6 (Gene Name=rpl6)