Structure of PDB 5ib7 Chain 88 Binding Site BS02

Receptor Information

>5ib7 Chain 88 (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

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): P4 R5 R6 K8 Y9 R10 K11 Q12 Q13 R14 G15 R16 L17 K18 K22 G24 Y26 A28 F29 A40 W41 Q46 A49 R56 K63 F65 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 I120 H123 K124 P126 K128
• Binding residue (residue number reindexed from 1): P4 R5 R6 K8 Y9 R10 K11 Q12 Q13 R14 G15 R16 L17 K18 K22 G24 Y26 A28 F29 A40 W41 Q46 A49 R56 K63 F65 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 I120 H123 K124 P126 K128

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:5ib7, PDBe:5ib7, PDBj:5ib7
• PDBsum: 5ib7
• PubMed: 27174928
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)