Structure of PDB 5v8i Chain 1G Binding Site BS01

Receptor Information

>5v8i Chain 1G (length=181) Species: 262724 (Thermus thermophilus HB27)

PLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

Ligand information

>5v8i Chain 1A (length=2862)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgucuaguccgcggccguggacccgaaaccgggcgagcu
agcccuggccagggugaagcuggggugagacccaguggaggcccgaaccg
gugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcua
accgagcccggagauagcugguucuccccgaaaugacuuuagggucagcc
ucaggcgcugacuggggccuguagagcacugauagggcuagggggcccac
cagccuaccaaacccugucaaacuccgaagggucccagguggagccuggg
agugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgag
accgccagcuaaggcccccaagucugggcuaagugguaaaggauguggcg
ccgcgaagacagccaggagguuggcuuagaagcagccauccuuuaaagag
ugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaucggggc
ucaagcccagcgccgaagcugcgggucugggggaugaccccaggcgguag
gggagcguucccgaugccgaugaaggccgacccgcgagggcggcuggagg
uaagggaagugcgaaugccggcaugaguaacgauaaagagggugagaauc
ccucucgccguaagcccaaggguuccuacgcaauggucgucagcguaggg
uuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgg
uuaauauuccggcccuucccgcaggugcgauggggggacgcucuaggcua
gggggaccggagccauggacgagcccggccagaagcgcagggugggaggu
aggcaaauccgccucccaaaagcucugcgugguggggaagcccgggugac
aaccccccgaagccagggagccaagaaaagccucuaagcacaaccugcgg
gaacccguaccgcaaaccgacacaggugggcgggugcaagagcacucagg
cgcgcgggagaacccucgccaaggaacucugcaaguuggccccguaacuu
cgggagaaggggugcucccuggggugaugagcuccggggagccgcaguga
acaggcucuggcgacuguuuaccaaaaacacagcucucugcgaacucgua
agaggagguauagggagcgacgcuugcccggugccggaaggucaagggga
ggggugcaagccccgaaccgaagccccggugaacggcggccguaacuaua
acgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacg
aaaagcguaacgaccggagcgcugucucggcgagggacccggugaaauug
aacuggccgugaagaugcggccuacccguggcaggacgaaaagaccccgu
ggagcuuuacugcagccugguguuggcucuuggucgcgccugcguaggau
aggugggagccugugaacccccgccuccgggugggggggaggcgccggug
aaauaccacccuggcgcggcugggggccuaacccucggauggggggacag
cgcuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacgga
ggcgcccaaagguccccucaggcgggacggaaauccgccggagagcgcaa
ggguagaagggggccugacugcgaggccugcaagccgagcaggggcgaaa
gccgggccuagugaaccgguggucccguguggaagggccaucgaucaacg
gauaaaaguuaccccggggauaacaggcugaucucccccgagcguccaca
gcggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcu
gaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgag
cuggguucagaacgucgugagacaguucggucucuauccgccacgggcgc
aggaggcuugaggggggcucuuccuaguacgagaggaccggaagggacgc
accucugguuucccagcugucccuccaggggcauaagcuggguagccaug
ugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaag
augaggccucccacggcagccgguaaggacccgggaagacgacccggugg
augggccggggguguaagcgccgcgaggcguugagccgaccggucccaau
cguccgaggucu

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

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): K36 V38 N40 L43 E45 T71 A73 K75 I77 F80 I88 R91 S124 F125 D126 R128 N132 L133 G134 L135 G154 M155 D156
• Binding residue (residue number reindexed from 1): K35 V37 N39 L42 E44 T70 A72 K74 I76 F79 I87 R90 S123 F124 D125 R127 N131 L132 G133 L134 G153 M154 D155

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5v8i, PDBe:5v8i, PDBj:5v8i
• PDBsum: 5v8i
• UniProt: Q72I16|RL5_THET2 Large ribosomal subunit protein uL5 (Gene Name=rplE)