Structure of PDB 6d90 Chain e Binding Site BS01

Receptor Information

>6d90 Chain e (length=128) Species: 9986 (Oryctolagus cuniculus)

AALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKG
QILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAH
NVSSKNRKAIVERAAQLAIRVTNPNARL

Ligand information

>6d90 Chain 5 (length=3594)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugccggcggggcgga
ucucccgcucccgucggcgggggaccgccccccggccggcgaccggccgc
cgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacg
gcugggaaggcccggcggggaagguggcccgggggccccggguguuacag
cccgccccggcagcagcagcucgccgaaucccggggccgagggagcgaga
cccgugcgccgcgcucuccccccucgggggggccgggccaccccucccac
ggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgcc
gucgggcccggggggccacgcgucccccgcgagcgcacggggucggcggc
gaugucggcuacccacccgacccgucuugaaacacggaccaaggagucua
acacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaaggu
gaaggccggcgccgccggccgaggugggaucccgaggccuuccaguccgc
cgagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagc
acgagcgcacguguuaggacccgaaagauggugaacuaugccugggcagg
gcgaagccagaggaaacucugguggagguccguagcgguccugacgugcg
aaucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucu
aguagcugguucccuccaaaguuucccucaggauagcuggcgcucuccgc
aguuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgauc
ucaaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggugu
ggagccgggcguggaaugcgagugccuagugggccacuuuugguaagcag
aacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccg
acgcucaucagaccccagaaaagguguugguugauauagacagcaggaug
guggccauggaagucggaauccgcuaaggaguguguaacaacucaccugc
cgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauac
ccggccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgc
uacgccgcgacgaguaggagggccgcugcggugagccuugaagccuaggg
cgcgggcccggguggagccgccgcaggugcagaucuuggugguaguagca
aauauucaaacgagaacuuugaaggccgaaguggagaaggguuccaugug
aacagcaguugaacaugggucagucgguccugagagaugggcgagcgccg
uuccgaagggacgggcgauggccuccguugcccucagccgaucgaaaggg
agucggguucagauccccgaauccggaguggcggagaugggcgccgcgag
gcguccagugcgguaacgcgaccgaucccggagaagccggcgggagcccc
ggggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguu
cgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggc
guccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaa
ucucgcgccgggccguacccauauccgcagcaggucuccaaggugaacag
ccucuggcauguuggaacaauguagguaagggaagucggcaagccggauc
cguaacuucgggauaaggauuggcucuaagggcuggcagccgacuuagaa
cuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcg
aaggcccgcggcggguguugacgcgaugugauuucugcccagugcucuga
augucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaac
uaugacucucuuaagguagccaaaugccucgucaucuaauuagugacgcg
caugaauggaugaacgagauucccacugucccuaccuacuauccagcgaa
accacagccaagggaacgggcuuggcggaaucagcggggaaagaagaccc
uguugagcuugacucuagucuggcacggugaagagacaugagagguguag
aauaagugggaggcccgggccgccggugaauaccacuacucugaucguuu
uuucacugacccggugaggcgggggggcgagccgggcucucgcuucuggc
gccaagcgcccggccggccgggcgcgacccgcuccggggacagugccagg
uggggaguuugacuggggcgguacaccugucaaacgguaacgcagguguc
cuaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaa
aagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggg
gccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaa
aguuaccacagggauaacuggcuuguggcggccaagcguucauagcgacg
ucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaa
uucaccaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugauguguuguu
gccaugguaauccugcucaguacgagaggaaccgcagguucagacauuug
guguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauag
cgccggagccucgguuggccucggauagccggucccccgccgggguccgg
ugcggagagcccuucgucccgggaaacggggcggccggaaagggggccgc
ccucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacc
auucguagacgaccugcuucugggucgggguuucguacguagcagagcag
cugcugcgaucuauugaaagucagcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
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....>>>>.....((......<<<.....))>>>.....>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...<<<<<..(((((.>>>>>..>>>........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<....<<<<<<<.<<<<<.<<<<<<<.
<<<<<<<<<......>>>>>>>>>>>>>>>>>>>>>>>>>...>>>..>>
>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<<<<
<<...<<..<<<..<..<<<......<<<<<<<<.>>>>>>>>.......
>>>..>..>>>.........>>>>>>..>>>>>>>>>>>...........
.{............<...<<<<<<..>>>>>>....<<<..<<<.<<<<<
<<<<<<<<<<<<<<<<<<.<<<<..>>>>.>>>>>>.>>>.>>>>>>>>>
>>.>>>...>>>>>.>................>.........>>.>>>>>
....>>>>...>>>>>>>>..<<<<........>>>><<<<<<....<<<
<<<<<<<<<<..<<<...<<<<.....>>>>.....>>>...<<....>>
...<<<<<<.....>>>>>>..<<<<<...<<<..<<<...(((.[[.>>
>..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>
....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<
<....<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<......
..>>>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>.
.....>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<...<<
<.<<<<<<<<....<<<....<<<..<.<<<..<<<<.<.........>.
>>>>>>>.>..>>>..>.>>....>>>>>>...<<<<<<<<<.<......
>>>>>>>>>>....>>>>>>>>>>>>.>>>..<<<<.<<<<<.....>>>
>>.>>>>....<<<......>>>...<<<<<<<...<<<(((.......<
<<<<.....<<..........<<<.<<<<<<<<<<.......<<<<<.<<
....<<.........>>....>>.........<<......>>...>>>>>
...>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>
>>>>><<<<<<.<<<........}...........]].))).........
...>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<
<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<<....<<.
....<<<<<.........>>>>>.<<<.....<<<<<.<<...<<<<<<.
..<<.....>>.>>>>>>....((<<<<<<...<<....<<<....>>>.
.........<<.<<<<<.<<.....>>.>>>>>>>......>>....>>>
..<<<<<........>>>>>))<<<<....<<<<<...<<<<<<<....>
>>>>>>...<<<....>>>......<<<<<<<...<<<<<<<<<<<<.<<
<<<<<<<<..[[[..>>>>>>.....<<<<.<<<<.<<<<.....<<<..
...>>>.....>>>>>>>>..>>>>......<<<<<<<.......>>>>>
>>>>>>...>>>>>>>>>>>>.........>>>>>>>.............
>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<.....>
>>>..>>>....<<<<.....<<<<<<<.<<.........<.....<<<<
<.....<..>......>>>>><<.<<<<<<<<<<...>>>>..>>>>>>.
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
...<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<...
.<<<....<<<<......>>>.>...>>>.>>>>..>>>>><<<<<<...
....>>>>>>........<...........<<<<<.......>>>>>...
..>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>...
>>>....<<<<<........>>>>>....<<<<<..<<<.<<......<<
<<.<<<<<<..<<<<<.<<<<<<<<..<<<<<<<<<<...<<<.......
....<<<.<..<<<<..>>>>...........>.>>>..>>>....>>>>
>>>>>>...<<<<<.....<<<<..<<...<<<>>.>..>>.........
.....<<<<<<<<<..>>>>>>>>>..>>>>..>>>>>.....>>>>>>>
>..>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>..
..>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>
>)))]......<<<<<<..<<<...))))).>>>>>>>>>..........
>>>>..>>>>>>.......<<.<...<<<<<<...<<.......>>...>
>>>>>....>.>.>.........<<<.<<<<<<..<.<.<<<<<......
>>>>>.>...>.<<<.........>>>.....>>>>>..>...>>>....
...<<<<<<<....>>>.>>>>....>>..>>>.>>>>>.....<<<<<<
.<..<<<..<.<<<<<.................>>>>>.><<<<....<<
<<....<<.<<<<<<.]]]..>>>>..>>.>>...>>>>...>>>><<<<
....<<<<<...........>>>>>....>>>>.>>>...>.>>>>>>.<
<<<<<<..<<<<....<<<........<<<<<..<<<<<.>>>>>.>>>>
>.......>>>...<<<..<<<<....<<.<<<<<<........>>>>>>
..>>...>>>>..>>>..............>>>>..>.>>>>>>..<<<<
.<.............>....<<.<<<<<<<.<<.....<<<<.<..<<<<
<.>>>>>..>>>>>....>>....>>>>.>>>.>>..>>>.>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d90 Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R5 K15 T17 K18 K19 F20 R22 H23 Q24 D26 R27 Y28 K30 I31 N34 W35 R36 K37 R39 G40 I41 D42 N43 R44 R46 R47 R48 F49 K50 G51 Q52 P56 N57 I58 G59 Y60 G61 S62 N63 K64 K67 H68 L70 L78 E98 A100 H101 S104 A127
• Binding residue (residue number reindexed from 1): R4 K14 T16 K17 K18 F19 R21 H22 Q23 D25 R26 Y27 K29 I30 N33 W34 R35 K36 R38 G39 I40 D41 N42 R43 R45 R46 R47 F48 K49 G50 Q51 P55 N56 I57 G58 Y59 G60 S61 N62 K63 K66 H67 L69 L77 E97 A99 H100 S103 A126

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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:6d90, PDBe:6d90, PDBj:6d90
• PDBsum: 6d90
• PubMed: 29856316
• UniProt: G1TUN8|RL32_RABIT Large ribosomal subunit protein eL32 (Gene Name=RPL32)