Structure of PDB 5v8i Chain 1W Binding Site BS01

Receptor Information

>5v8i Chain 1W (length=112) Species: 262724 (Thermus thermophilus HB27)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHG

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): K4 I6 A7 R8 Y9 R11 S13 R15 K16 R18 N40 K41 R42 Y45 K49 S53 A56 N57 N60 N61 H62 D77 E78 P80 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98
• Binding residue (residue number reindexed from 1): K4 I6 A7 R8 Y9 R11 S13 R15 K16 R18 N40 K41 R42 Y45 K49 S53 A56 N57 N60 N61 H62 D77 E78 P80 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5v8i, PDBe:5v8i, PDBj:5v8i
• PDBsum: 5v8i
• UniProt: Q72I09|RL22_THET2 Large ribosomal subunit protein uL22 (Gene Name=rplV)