Structure of PDB 5ib7 Chain 58 Binding Site BS01

Receptor Information

>5ib7 Chain 58 (length=137) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEK

Ligand information

>5ib7 Chain 1H (length=2860)

aagaugguaagggcccacgguggaugccucggcacccgagccgaugaagg
acguggcuaccugcgauaagccagggggagccgguagcgggcguggaucc
cuggauguccgaaugggggaacccggccggcgggaacgccggucaccgcg
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgcaaacgggggccgaaaaguccgcggcc
guggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggug
agacccaguggaggcccgaaccggugggggaugcaaaccccucggaugag
cuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucucc
ccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagagc
acugauagggcuaggggccuccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggggagcucauuuaaagagugc
gcucacuggucgaguggcgccgcgccgaaaaugaucggggcuuaagccca
gcgccgaagcugcgggucugggggaugaccccaggcgguaggggagcguu
cccgaugccgaugaaggccgacccgcgagggcggcuggagguaagggaag
ugcgaaugccggcaugaguaacgauaaagagggugagaaucccucucgcc
guaagcccaaggguuccuacgcaauggucgucagcguaggguuaggcggg
accuaaggugaagccgaaaggcguagccgaagggcagccgguuaauauuc
cggcccuucccgcaggugcgauggggggacgcucuaggcuagggggaccg
gagccauggacgagcccggccagaagcgcagggugggagguaggcaaauc
cgccucccaacaagcucugcgugguggggaagcccguacgggugacaacc
ccccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaac
ccguaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcg
cgggagaacccucgccaaggaacucugcaaguuggccccguaacuucggg
agaaggggugcucccuggggugaugagccccggggagccgcagugaacag
gcucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaagag
gagguauagggagcgacgcuugcccggugccggaaggucaaggggagggg
ugcaagccccgaaccgaagccccggugaacggcggccguaacuauaacgg
uccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaa
gcguaacgaccggagcgcugucucggcgagggacccggugaaauugaacu
ggccgugaagaugcggccuacccguggcaggacgaaaagaccccguggag
cuuuacugcagccugguguuggcucuuggucgcgccugcguaggauaggu
gggagccugugaacccccgccuccgggugggggggaggcgccggugaaau
accacccuggcgcggcugggggccuaacccucggauggggggacagcgcu
uggcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcg
cccaaagguccccucaggcgggacggaaauccgccggagagcgcaagggu
agaagggggccugacugcgaggccugcaagccgagcaggggcgaaagccg
ggccuagugaaccgguggucccguguggaagggccaucgaucaacggaua
aaaguuaccccggggauaacaggcugaucucccccgagcguccacagcgg
cggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaag
aaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugg
guucagaacgucgugagacaguucggucucuauccgccacgggcgcagga
ggcuugaggggggcucuuccuaguacgagaggaccggaagggacgcaccu
cugguuucccagcugucccuccaggggcauaagcuggguagccaugugcg
gaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaagauga
ggccucccacggcgagccgguaaggacccgggaagaccacccgguggaug
ggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgu
ccgaggucuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ib7 The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
• Resolution: 2.99 Å
• Binding residue (original residue number in PDB): K2 T3 L23 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 K70 R74 Y75 S76 Y78 G80 L82 K89 R97 E100 H101 A102 G105 M106 P108 P111 L112 R114 K118 P129 Q131
• Binding residue (residue number reindexed from 1): K2 T3 L23 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 K70 R74 Y75 S76 Y78 G80 L82 K89 R97 E100 H101 A102 G105 M106 P108 P111 L112 R114 K118 P129 Q131

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ib7, PDBe:5ib7, PDBj:5ib7
• PDBsum: 5ib7
• PubMed: 27174928
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)