Structure of PDB 4xej Chain AL23 Binding Site BS01

Receptor Information

>4xej Chain AL23 (length=92) Species: 262724 (Thermus thermophilus HB27)

TAYDVILAPVLSEKAYAGFAEGKYTFWVHPKATKTEIKNAVETAFKVKVV
KVNTLHVRGKKKRLGRYLGKRPDRKKAIVQVAPGQKIEALEG

Ligand information

>4xej Chain A23S (length=2876)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccagggguuggcuuagaagcagccauccu
uuaaagagugcguaauagcuccuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaaaagcucugcgugguggggaagccc
guacgggugacaaccccccgaagccagggagccaagaaaagccucuaagc
acaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaa
gagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguugg
ccccguaacuucgggagaaggggugcucccuggggugaugagcuccgggg
agccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucu
gcgaacucguaagaggagguauagggagcgacgcuugcccggugccggaa
ggucaaggggaggggugcaagccccgaaccgaagccccggugaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacc
cggugaaauugaacuggccgugaagaugcggccuacccguggcaggacga
aaagaccccguggagcuuuacugcagccugguguuggcucuuggucgcgc
cugcguaggauaggugggagccugugaacccccgccuccggguggggggg
aggcgccggugaaauaccacccuggcgcggcuggggccuaacccucggau
ggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaa
agguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccg
gagagcgcaaggguagaagggggccugacugcgaggccugcaagccgagc
aggggcgaaagccgggccuagugaaccgguggucccguguggaagggcca
ucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccg
agcguccacagcggcggggagguuuggcaccucgaugucggcucgucgca
uccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagc
ggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccg
ccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccg
gaagggacgcaccucugguuucccagcugucccuccaggggcauaagcug
gguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagc
ccgccccaagaugaggccucccacggcgucaagccgguaaggacccggga
agacuacccgguggaugggccggggguguaagcgccgcgaggcguugagc
cgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4xej Initiation of translation in bacteria by a structured eukaryotic IRES RNA.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): S14 K16 K25 H31 T35 K36 T37 E38 N41 K53 N55 T56 L57 H58 R60 K62 K64 R65 L66 Y69 L70 G71 K72 R73 P74 D75 K77 K78 I80
• Binding residue (residue number reindexed from 1): S12 K14 K23 H29 T33 K34 T35 E36 N39 K51 N53 T54 L55 H56 R58 K60 K62 R63 L64 Y67 L68 G69 K70 R71 P72 D73 K75 K76 I78

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4xej, PDBe:4xej, PDBj:4xej
• PDBsum: 4xej
• PubMed: 25652826
• UniProt: Q72I06|RL23_THET2 Large ribosomal subunit protein uL23 (Gene Name=rplW)