Structure of PDB 6oxa Chain Y1 Binding Site BS01

Receptor Information

>6oxa Chain Y1 (length=93) Species: 300852 (Thermus thermophilus HB8)

SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRV
RVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKEL

Ligand information

>6oxa Chain YA (length=2875)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggacaccgaauc
cccagccuagccgaagcuguugggaagcagcgccagagagggugaaagcc
ccguaggcgaaagguggggggauaggugaggguacccgaguaccccgugg
uucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagua
cuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaa
ccccgggaggggagugaaauagagccugaaaccgugggcuuacaagcagu
cacggccccgcaagggguuguggcgugccuauugaagcaugagccggcga
cucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaac
cgaguccgaacagggcgcaaaguccgcggccguggacccgaaaccgggcg
agcuagcccuggccagggugaagcuggggugagacccaguggaggcccga
accggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaa
gcuaaccgagcccggagauagcugguucuccccgaaaugacuuuaggguc
agccucaggcgcugacuggggccuguagagcacugauagggcuagggggc
ccaccagccuaccaaacccugucaaacuccgaagggucccagguggagcc
ugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaac
cgagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugu
ggcgccgcgaagacagccaggagguuggcuuagaagcagccauccuuuaa
agagugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaucg
gggcuuaagcccagcgccgaagcugcgggucugggggaugaccccaggcg
guaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcug
gagguaagggaagugcgaaugccggcaugaguaacgauaaagagggugag
aaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcgu
aggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcag
ccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucuag
gcuagggggaccggagccauggacgagcccggccagaagcgcaggguggg
agguaggcaaauccgccucccaacaagcucugcgugguggggaagcccgu
acgggugacaaccccccgaagccagggagccaagaaaagccucuaagcac
aaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaaga
gcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcc
ccguaacuucgggagaaggggugcucccuggggugaugagccccggggag
ccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugc
gaacucguaagaggagguauagggagcgacgcuugcccggugccggaagg
ucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggcc
guaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccg
accugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccg
gugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaa
agaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccu
gcguaggauaggugggagccugugaacccccgccuccgggugggggggag
gcgccggugaaauaccacccuggcgcggcugggggccuaacccucggaug
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccacggcgucaagccgguaaggacccgggaa
gaccacccgguggaugggccggggguguaagcgccgcgaggcguugagcc
gaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oxa Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): S2 K3 R11 I13 A15 N16 R20 R21 A24 K25 G29 V30 K32 T34 T35 I37 K39 R40 R41 Q42 Y43 P44 N45 Q47 R50 H66 K69 R76 K78 E93
• Binding residue (residue number reindexed from 1): S1 K2 R10 I12 A14 N15 R19 R20 A23 K24 G28 V29 K31 T33 T34 I36 K38 R39 R40 Q41 Y42 P43 N44 Q46 R49 H65 K68 R75 K77 E92

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:6oxa, PDBe:6oxa, PDBj:6oxa
• PDBsum: 6oxa
• PubMed: 31501867
• UniProt: P60494|RL28_THET8 Large ribosomal subunit protein bL28 (Gene Name=rpmB)