Structure of PDB 6oxi Chain Y5 Binding Site BS01

Receptor Information

>6oxi Chain Y5 (length=59) Species: 300852 (Thermus thermophilus HB8)

AKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGY
YAGRKVLEV

Ligand information

>6oxi Chain YA (length=2878)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuugcgcggggggaaccuggggaacugaaacaucucaguacccagaggag
aggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagc
cuaaaccguccggcuuguccgggcggggucguggggcccucggacaccga
auccccagccuagccgaagcuguugggaagcagcgccagagagggugaaa
gccccguaggcgaaagguggggggauaggugaggguacccgaguaccccg
ugguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaa
guacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaa
gaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagc
agucacggccccgcaagggguuguggcgugccuauugaagcaugagccgg
cgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggga
aaccgaguccgaacagggcgcaaaguccgcggccguggacccgaaaccgg
gcgagcuagcccuggccagggugaagcuggggugagacccaguggaggcc
cgaaccggugggggaugcaaaccccucggaugagcuggggcuaggaguga
aaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuuagg
gucagccucaggcgcugacuggggccuguagagcacugauagggcuaggg
ggcccaccagccuaccaaacccugucaaacuccgaagggucccaggugga
gccugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaac
aaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaagga
uguggcgccgcgaagacagccaggagguuggcuuagaagcagccauccuu
uaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaacaagcucugcgugguggggaagcc
cguacgggugacaaccccccgaagccagggagccaagaaaagccucuaag
cacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugca
agagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguug
gccccguaacuucgggagaaggggugcucccuggggugaugagccccggg
gagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucuc
ugcgaacucguaagaggagguauagggagcgacgcuugcccggugccgga
aggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggac
ccggugaaauugaacuggccgugaagaugcggccuacccguggcaggacg
aaaagaccccguggagcuuuacugcagccugguguuggcucuuggucgcg
ccugcguaggauaggugggagccugugaacccccgccuccgggugggggg
gaggcgccggugaaauaccacccuggcgcggcugggggccuaacccucgg
auggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccua
aaagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgc
cggagagcgcaaggguagaagggggccugacugcgaggccugcaagccga
gcaggggcgaaagccgggccuagugaaccgguggucccguguggaagggc
caucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccc
cgagcguccacagcggcggggagguuuggcaccucgaugucggcucgucg
cauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaa
gcggcacgcgagcuggguucagaacgucgugagacaguucggucucuauc
cgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggac
cggaagggacgcaccucugguuucccagcugucccuccaggggcauaagc
uggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaa
gcccgccccaagaugaggccucccacggcgucaagccgguaaggacccgg
gaagaccacccgguggaugggccggggguguaagcgccgcgaggcguuga
gccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oxi Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
• Resolution: 3.495 Å
• Binding residue (original residue number in PDB): A2 K3 H4 P5 V6 P7 K8 K9 K10 T11 S12 K13 A14 R15 R16 D17 A18 R19 R20 S21 H22 H23 T29 V31 P42 H43 Y52 A53
• Binding residue (residue number reindexed from 1): A1 K2 H3 P4 V5 P6 K7 K8 K9 T10 S11 K12 A13 R14 R15 D16 A17 R18 R19 S20 H21 H22 T28 V30 P41 H42 Y51 A52

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6oxi, PDBe:6oxi, PDBj:6oxi
• PDBsum: 6oxi
• PubMed: 31501867
• UniProt: P80339|RL32_THET8 Large ribosomal subunit protein bL32 (Gene Name=rpmF)