Structure of PDB 8t8c Chain 2Y Binding Site BS01

Receptor Information

>8t8c Chain 2Y (length=107) Species: 300852 (Thermus thermophilus HB8)

MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVR
VSPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCA
KCGGALD

Ligand information

>8t8c Chain 2A (length=2867)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucuggggccccaggcg
guaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcug
gagguaagggaagugcgaaugccggcaugaguaacgauaaagagggugag
aaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcgu
aggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcag
ccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucuag
gcuagggggaccggagccauggacgagcccggccagaagcgcaggguggg
agguaggcaaauccgccucccaacaagcucugcgugguggggaagcccgc
gggugacaaccccccgaagccagggagccaagaaaagccucuaagcacaa
ccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagagc
acucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcccc
guaacuucgggagaaggggugcucccuggggugaugagccccggggagcc
gcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcga
acucguaagaggagguauagggagcgacgcuugcccggugccggaagguc
aaggggaggggugcaagccccgaaccgaagccccggugaacggcggccgu
aacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgac
cugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccggu
gaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaag
accccguggagcuuuacugcagccugguguuggcucuuggucgcgccugc
guaggauaggugggagccugugaacccccgccuccgggugggggggaggc
gccggugaaauaccacccuggcgcggcugggggccuaacccucggauggg
gggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagg
uaacggaggcgcccaaagguccccucaggcgggacggaaauccgccggag
agcgcaaggguagaagggggccugacugcgaggccugcaagccgagcagg
ggcgaaagccgggccuagugaaccgguggucccguguggaagggccaucg
aucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagc
guccacagcggcggggagguuuggcaccucgaugucggcucgucgcaucc
uggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggc
acgcgagcuggguucagaacgucgugagacaguucggucucuauccgcca
cgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaa
gggacgcaccucugguuucccagcugucccuccaggggcauaagcugggu
agccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccg
ccccaagaugaggccucccggcagccgguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8t8c Practical Synthesis of N -Formylmethionylated Peptidyl-tRNA Mimics.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): M1 K4 H6 K8 K9 S17 G18 K19 V30 P32 K46 K47 A48 R50 G58 G59 F60 K63 H68 S70 K71 R73 R84 R86 K87 K95 K101
• Binding residue (residue number reindexed from 1): M1 K4 H6 K8 K9 S17 G18 K19 V30 P32 K46 K47 A48 R50 G58 G59 F60 K63 H68 S70 K71 R73 R84 R86 K87 K95 K101

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:8t8c, PDBe:8t8c, PDBj:8t8c
• PDBsum: 8t8c
• PubMed: 37433044
• UniProt: Q5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)