Structure of PDB 5v8i Chain 2S Binding Site BS01

Receptor Information

>5v8i Chain 2S (length=110) Species: 262724 (Thermus thermophilus HB27)

RLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSAS
SLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKALA
EGAREGGLEF

Ligand information

>5v8i Chain 2A (length=2858)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgucuaguccgcggccguggacccgaaaccgggcgag
cuagcccuggccagggugaagcuggggugagacccaguggaggcccgaac
cggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagc
uaaccgagcccggagauagcugguucuccccgaaaugacuuuagggucag
ccucaggcgcugacuggggccuguagagcacugauagggcuagggggccc
accagccuaccaaacccugucaaacuccgaagggucccagguggagccug
ggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccg
agaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugugg
cgccgcgaagacagccaggagguggcuuagaagcagccauccuuuaaaga
gugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaucgggg
cucaagcccagcgccgaagcugcgggucuggggccccaggcgguagggga
gcguucccgaugccgaugaaggccgacccgcgagggcggcuggagguaag
ggaagugcgaaugccggcaugaguaacgauaaagagggugagaaucccuc
ucgccguaagcccaaggguuccuacgcaauggucgucagcguaggguuag
gcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaa
uauuccggcccuucccgcaggugcgauggggggacgcucuaggcuagggg
gaccggagccauggacgagcccggccagaagcgcagggugggagguaggc
aaauccgccucccaaaagcucugcgugguggggaagcccgcgggugacaa
ccccccgaagccagggagccaagaaaagccucuaagcacaaccugcggga
acccguaccgcaaaccgacacaggugggcgggugcaagagcacucaggcg
cgcgggagaacccucgccaaggaacucugcaaguuggccccguaacuucg
ggagaaggggugcucccuggggugaugagcuccggggagccgcagugaac
aggcucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaag
aggagguauagggagcgacgcuugcccggugccggaaggucaaggggagg
ggugcaagccccgaaccgaagccccggugaacggcggccguaacuauaac
gguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaa
aagcguaacgaccggagcgcugucucggcgagggacccggugaaauugaa
cuggccgugaagaugcggccuacccguggcaggacgaaaagaccccgugg
agcuuuacugcagccugguguuggcucuuggucgcgccugcguaggauag
gugggagccugugaacccccgccuccgggugggggggaggcgccggugaa
auaccacccuggcgcggcugggggccuaacccucggauggggggacagcg
cuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacggagg
cgcccaaagguccccucaggcgggacggaaauccgccggagagcgcaagg
guagaagggggccugacugcgaggccugcaagccgagcaggggcgaaagc
cgggccuagugaaccgguggucccguguggaagggccaucgaucaacgga
uaaaaguuaccccggggauaacaggcugaucucccccgagcguccacagc
ggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcuga
agaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcu
ggguucagaacgucgugagacaguucggucucuauccgccacgggcgcag
gaggcuugaggggggcucuuccuaguacgagaggaccggaagggacgcac
cucugguuucccagcugucccuccaggggcauaagcuggguagccaugug
cggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaagau
gaggccucccggcagccgguaaggacccgggaagacgacccgguggaugg
gccggggguguaagcgccgcgaggcguugagccgaccggucccaaucguc
cgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v8i Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): R3 L4 A6 R9 R10 F12 R13 N16 R17 I18 T21 R23 F87 R89 Y94 R106 F112
• Binding residue (residue number reindexed from 1): R1 L2 A4 R7 R8 F10 R11 N14 R15 I16 T19 R21 F85 R87 Y92 R104 F110

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5v8i, PDBe:5v8i, PDBj:5v8i
• PDBsum: 5v8i
• UniProt: Q72I20|RL18_THET2 Large ribosomal subunit protein uL18 (Gene Name=rplR)