Structure of PDB 5ibb Chain A5 Binding Site BS01

Receptor Information

>5ibb Chain A5 (length=111) Species: 300852 (Thermus thermophilus HB8)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKH

Ligand information

>5ibb Chain 14 (length=2810)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucguggggcccucggacaccgaa
uccccagccuagccgaagcuguugggaagcagcgccagagagggugaaag
ccccguaggcgaaagguggggggauaggugaggguacccgaguaccccgu
gguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaag
uacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaag
aaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagca
gucacggccccgcaagggguuguggcgugccuauugaagcaugagccggc
gacucacggucgugggcgagcuuaagccguugaggcggaggcguagggaa
accgaguccgaacagggcgcaaacggcgaaaaguccgcggccguggaccc
gaaaccgggcgagcuagcccuggccagggugaagcuggggugagacccag
uggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcu
aggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaug
acuuuagggucagccucaggcgcugacuggggccuguagagcacugauag
ggcuacaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cggacaggaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgc
cgaagcugcgggucugggggaugaccccaggcgguaggggagcguucccg
augccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcg
aaugccggcaugaguaacgauaaagagggugagaaucccucucgccguaa
gcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccu
aaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggc
ccuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagc
cauggacgagcccggccagaagcgcagggugggagguaggcaaauccgcc
ucccaacaagcucugcgugguggggaagcccguacgggugacaacccccc
gaagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgu
accgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggg
agaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaa
ggggugcucccuggggugaugagccccggggagccgcagugaacaggcuc
uggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggagg
uauagggagcgacgcuugcccggugccggaaggucaaggggaggggugca
agccccgaaccgaagccccggugaacggcggccguaacuauaacgguccu
aagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgu
aacgaccggagcgcugucucggcgagggacccggugaaauugaacuggcc
gugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuu
acugcagccugguguuggcucuuggucgcgccuguaggauaggugggagc
cugugaacccccgccuccgggugggggggaggcgccggugaauaccaccc
uggcgcggcugggggccuaacccucggauggggggacagcgcuuggcggg
caguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaag
guccccucaggcgggacggaaauccgccggagagcgcaaggguagaaggg
ggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuag
ugaaccgguggucccguguggaagggccaucgaucaacggauaaaaguua
ccccggggauaacaggcugaucucccccgagcguccacagcggcggggag
guuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggucc
caaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucaga
acgucgugagacaguucggucucuauccgccacgggcgcaggaggcuuga
ggggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuu
cccagcugucccuccaggggcauaagcuggguagccaugugcggaaggga
uaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucc
cacggcgucaagccgguaaggacccgggaagaccacccgguggaugggcc
ggggguguaagcgccgcgaggcguugagccgaccggucccaaucguccga
ggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ibb The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): K4 I6 A7 R8 Y9 R11 S13 R15 K16 R25 K41 R42 Y45 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 P80 K83 R84 P87 R88 A89 R90 G91 R92 D94 I96 K97 K98 R99 H102
• Binding residue (residue number reindexed from 1): K4 I6 A7 R8 Y9 R11 S13 R15 K16 R25 K41 R42 Y45 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 P80 K83 R84 P87 R88 A89 R90 G91 R92 D94 I96 K97 K98 R99 H102

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ibb, PDBe:5ibb, PDBj:5ibb
• PDBsum: 5ibb
• PubMed: 27174928
• UniProt: Q5SHP3|RL22_THET8 Large ribosomal subunit protein uL22 (Gene Name=rplV)