Structure of PDB 6gsk Chain J8 Binding Site BS02

Receptor Information

>6gsk Chain J8 (length=96) Species: 300852 (Thermus thermophilus HB8)

SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRV
RVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKL

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

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

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): S2 K3 K10 I13 V14 A15 N16 I18 Q19 R20 R21 K25 G28 G29 V30 K32 K33 T34 T35 K39 R40 R41 Q42 Y43 P44 N45 Q47 R52 H66 K69 K81 G84
• Binding residue (residue number reindexed from 1): S1 K2 K9 I12 V13 A14 N15 I17 Q18 R19 R20 K24 G27 G28 V29 K31 K32 T33 T34 K38 R39 R40 Q41 Y42 P43 N44 Q46 R51 H65 K68 K80 G83

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:6gsk, PDBe:6gsk, PDBj:6gsk
• PDBsum: 6gsk
• PubMed: 29931292
• UniProt: P60494|RL28_THET8 Large ribosomal subunit protein bL28 (Gene Name=rpmB)