Structure of PDB 4lsk Chain RW Binding Site BS01

Receptor Information

>4lsk Chain RW (length=113) Species: 300852 (Thermus thermophilus HB8)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHGK

Ligand information

>4lsk Chain RA (length=2882)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccgcaagggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcaagcgcaaaguccgcggccguggacccgaaa
ccgggcgagcuagcccuggccagggugaagcuggggugagacccagugga
ggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagga
gugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuu
uagggucagccucaggcgcugacuggggccuguagagcacugauagggcu
agggggcccaccagccuaccaaacccugucaaacuccgaagggucccagg
uggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcgg
gaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaa
aggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccau
ccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacc
ccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagg
gcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaaga
gggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucg
ucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccga
agggcagccgguuaauauuccggcccuucccgcaggugcgauggggggac
gcucuaggcuagggggaccggagccauggacgagcccggccagaagcgca
gggugggagguaggcaaauccgccucccaacaagcucugcguggugggga
agcccguacgggugacaaccccccgaagccagggagccaagaaaagccuc
uaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcggg
ugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaa
guuggccccguaacuucgggagaaggggugcucccuggggugaugagccc
cggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagc
ucucugcgaacucguaagaggagguauagggagcgacgcuugcccggugc
cggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgag
ggacccggugaaauugaacuggccgugaagaugcggccuacccguggcag
gacgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggu
cgcgccugcguaggauaggugggagccugugaacccccgccuccgggugg
gggggaggcgccggugaaauaccacccuggcgcggcugggggccuaaccc
ucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccu
ccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaau
ccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaag
ccgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagcguccacagcggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccucccacggcgucaagccgguaaggac
ccgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcg
uugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4lsk Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.
• Resolution: 3.48001 Å
• Binding residue (original residue number in PDB): K4 A5 I6 A7 R8 Y9 R11 S13 R15 K16 R18 N40 K41 R42 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 P80 R84 P87 R88 A89 R90 G91 A93 D94 I96 K98 R99
• Binding residue (residue number reindexed from 1): K4 A5 I6 A7 R8 Y9 R11 S13 R15 K16 R18 N40 K41 R42 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 P80 R84 P87 R88 A89 R90 G91 A93 D94 I96 K98 R99

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:4lsk, PDBe:4lsk, PDBj:4lsk
• PDBsum: 4lsk
• PubMed: 25128388
• UniProt: Q5SHP3|RL22_THET8 Large ribosomal subunit protein uL22 (Gene Name=rplV)