Structure of PDB 4wzo Chain 15 Binding Site BS01

Receptor Information

>4wzo Chain 15 (length=138) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>4wzo Chain 14 (length=2877)

aagaugguaagggcccacgguggaugccucggcacccgagccgaugaagg
acguggcuaccugcgauaagccagggggagccgguagcgggcguggaucc
cuggauguccgaaugggggaacccggccggcgggaacgccggucaccgcg
cuugcgcggggggaaccuggggaacugaaacaucucaguacccagaggag
aggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagc
cuaaaccguccggcuuguccgggcggggucguggggcccucggacaccga
auccccagccuagccgaagcuguugggaagcagcgccagagagggugaaa
gccccguaggcgaaagguggggggauaggugaggguacccgaguaccccg
ugguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaa
guacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaa
gaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagc
agucacggccccgcaagggguuguggcgugccuauugaagcaugagccgg
cgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggga
aaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaagucc
gcggccguggacccgaaaccgggcgagcuagcccuggccagggugaagcu
ggggugagacccaguggaggcccgaaccggugggggaugcaaaccccucg
gaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcugg
uucuccccgaaaugacuuuagggucagccucaggcgcugacuggggccug
uagagcacugauagggcuagggggcccaccagccuaccaaacccugucaa
acuccgaagggucccagguggagccugggagugagggcgcgagcgauaac
guccgcguccgagcgcgggaacaaccgagaccgccagcuaaggcccccaa
gucugggcuaagugguaaaggauguggcgccgcgaagacagccaggaugu
uggcuuagaagcagccugcguaauagcucacuggucgaguggcgccgcgc
cgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucuggggga
ugaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccg
cgagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgau
aaagagggugagaaucccucucgccguaagcccaaggguuccuacgcaau
ggucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcgua
gccgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggg
gggacgcucuaggcuagggggaccggagccauggacgagcccggccagaa
gcgcagggugggagguaggcaaauccgccucccaacaagcucugcguggu
ggggaagcccguacgggugacaaccccccgaagccagggagccaagaaaa
gccucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugg
gcgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacuc
ugcaaguuggccccguaacuucgggagaaggggugcucccuggggugaug
agccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaac
acagcucucugcgaacucguaagaggagguauagggagcgacgcuugccc
ggugccggaaggucaaggggaggggugcaagccccgaaccgaagccccgg
ugaacggcggccguaacuauaacgguccuaagguagcgaaauuccuuguc
ggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucg
gcgagggacccggugaaauugaacuggccgugaagaugcggccuacccgu
ggcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcuc
uuggucgcgccugcguaggauaggugggagccugugaacccccgccuccg
ggugggggggaggcgccggugaaauaccacccuggcgcggcugggggccu
aacccucggauggggggacagcgcuuggcgggcaguuugacuggggcggu
cgccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacg
gaaauccgccggagagcgcaaggguagaagggggccugacugcgaggccu
gcaagccgagcaggggcgaaagccgggccuagugaaccgguggucccgug
uggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcu
gaucucccccgagcguccacagcggcggggagguuuggcaccucgauguc
ggcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucg
cccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucg
gucucuauccgccacgggcgcaggaggcuugaggggggcucuuccuagua
cgagaggaccggaagggacgcaccucugguuucccagcugucccuccagg
ggcauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucu
aagcgggaagcccgccccaagaugaggccucccacgccgguaaggacccg
ggaagaccacccgguggaugggccggggguguaagcgccgcgaggcguug
agccgaccggucccaaucguccgaggu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wzo Structural insights into the translational infidelity mechanism.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): T3 V5 T22 L23 G24 R25 T28 R35 K37 N45 T63 K66 Q69 K70 T73 R74 Y75 S76 Y78 P79 K83 K89 H94 R97 H101 A102 G105 M106 L107 G110 P111 L112 R114 R115 F117 K118 Q131
• Binding residue (residue number reindexed from 1): T3 V5 T22 L23 G24 R25 T28 R35 K37 N45 T63 K66 Q69 K70 T73 R74 Y75 S76 Y78 P79 K83 K89 H94 R97 H101 A102 G105 M106 L107 G110 P111 L112 R114 R115 F117 K118 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:4wzo, PDBe:4wzo, PDBj:4wzo
• PDBsum: 4wzo
• PubMed: 26037619
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)