Structure of PDB 5ibb Chain 45 Binding Site BS02

Receptor Information

>5ibb Chain 45 (length=139) Species: 300852 (Thermus thermophilus HB8)

LMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAAR
VAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGR
VMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEA

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): P4 R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G23 Y26 F29 W41 Q46 A49 R56 K63 R67 F69 D71 Y74 K76 K77 E80 V81 R82 M83 G84 K85 K87 G88 R101 R119 H123 K124 P126 K128
• Binding residue (residue number reindexed from 1): P3 R4 R5 K7 Y8 K10 Q11 Q12 R13 G14 R15 K21 G22 Y25 F28 W40 Q45 A48 R55 K62 R66 F68 D70 Y73 K75 K76 E79 V80 R81 M82 G83 K84 K86 G87 R100 R118 H122 K123 P125 K127

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5ibb, PDBe:5ibb, PDBj:5ibb
• PDBsum: 5ibb
• PubMed: 27174928
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)