Structure of PDB 5ibb Chain C5 Binding Site BS01

Receptor Information

>5ibb Chain C5 (length=104) Species: 300852 (Thermus thermophilus HB8)

RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRV
SPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAK
CGGA

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): R2 K4 H6 K8 K9 S17 G18 K19 V30 P32 I44 V45 K46 K47 V49 F60 H68 S70 K71 R73 K81 T83 R84 V85 R86 N92
• Binding residue (residue number reindexed from 1): R1 K3 H5 K7 K8 S16 G17 K18 V29 P31 I43 V44 K45 K46 V48 F59 H67 S69 K70 R72 K80 T82 R83 V84 R85 N91

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:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ibb, PDBe:5ibb, PDBj:5ibb
• PDBsum: 5ibb
• PubMed: 27174928
• UniProt: Q5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)