Structure of PDB 6gsk Chain D8 Binding Site BS01

Receptor Information

>6gsk Chain D8 (length=100) Species: 300852 (Thermus thermophilus HB8)

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTP
VVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR

Ligand information

>6gsk Chain 1H (length=2811)

uaagggcccacgguggaugccucggcacccgagccgaugaaggacguggc
uaccugcgauaagccagggggagccgguagcgggcguggaucccuggaug
uccgaaugggggaacccggccggcgggaacgccggucaccgcgcuuuuug
cgcggggggaaccuggggaacugaaacaucucaguacccagaggagagga
aagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccuaa
accguccggcuuguccgggcggggucguggggcccucggacaccgaaucc
ccagccuagccgaagcuguugggaagcagcgccagagagggugaaagccc
cguaggcgaaagguggggggauaggugaggguacccgaguaccccguggu
ucguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguac
uccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaac
cccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguc
acggccccgcaagggguuguggcgugccuauugaagcaugagccggcgac
ucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaacc
gaguccgaacagggcgcaaacgggggccgaaaaguccgcggccguggacc
cgaaaccgggcgagcuagcccuggccagggugaagcuggggugagaccca
guggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggc
uaggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaau
gacuuuagggucagccucaggcgcugacuggggccuguagagcacugaua
gggcuaggccucaaacccugucaaacuccgaagggucccagguggagccu
gggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaacc
gagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugug
gcgccgcgaagacagccaggaaaugccucacuggucgaguggcgccgcgc
cgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucuggggga
ugaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccg
cgagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgau
aaagagggugagaaucccucucgccguaagcccaaggguuccuacgcaau
ggucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcgua
gccgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggg
gggacgcucuaggcuagggggaccggagccauggacgagcccggccagaa
gcgcagggugggagguaggcaaauccgccucccaacaagcucugcguggu
ggggaagcccguacgggugacaaccccccgaagccagggagccaagaaaa
gccucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugg
gcgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacuc
ugcaaguuggccccguaacuucgggagaaggggugcucccuggggugaug
agccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaac
acagcucucugcgaacucguaagaggagguauagggagcgacgcuugccc
ggugccggaaggucaaggggaggggugcaagccccgaaccgaagccccgg
ugaacggcggccguaacuauaacgguccuaagguagcgaaauuccuuguc
ggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucg
gcgagggacccggugaaauugaacuggccgugaagaugcggccuacccgu
ggcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcuc
uuggucgcgccugcguaggauaggugggagccuaacccccgccuccgggu
ggggggggcgccggugaaauaccacccuggcgcggcugggggccuaaccc
ucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccu
ccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaau
ccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaag
ccgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagcguccacagcggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccuccguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gsk Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria.
• Resolution: 3.36 Å
• Binding residue (original residue number in PDB): G8 G9 K10 K19 R21 E23 K24 K69 K74 F75 K76 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90 E93
• Binding residue (residue number reindexed from 1): G8 G9 K10 K19 R21 E23 K24 K69 K74 F75 K76 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90 E93

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6gsk, PDBe:6gsk, PDBj:6gsk
• PDBsum: 6gsk
• PubMed: 29931292
• UniProt: P60492|RL21_THET8 Large ribosomal subunit protein bL21 (Gene Name=rplU)