Structure of PDB 6zvk Chain y2 Binding Site BS01

Receptor Information

>6zvk Chain y2 (length=114) Species: 9986 (Oryctolagus cuniculus)

VQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPG
RLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQK
IVVKVLKAQAQSQK

Ligand information

>6zvk Chain e2 (length=3920)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgccccccguggggucggcgggggaccguccccc
gaccggcgaccggccgccgccgggcgcauuuccaccgcggcggugcgccg
cgaccggcuccgggacggcugggaaggcccggcggggaagguggcucggg
gggccccgcgggaccgaaaccccccccgaguguuacagcccccccggcag
cagcacucgccgaaucccggggccgagggagcgagacccgucgccgcgcu
cuccccccucccggcgcccacccggggcgcgccggcgucuccucgugggg
gggccgggccaccccucccacggcgcgaccgcucucccaccccucgucgg
ggggcggggcggacuguccccagugcgccccgggcgggucgcgccgucgg
gcccgggggagguucucucggggccacgcgcgcgucccccgaagaggggg
acggcggagcgagcgcacggggucggcggcgacgucggcuacccacccga
cccgucuugaaacacggaccaaggagucuaacacgugcgcgagucggggg
cucgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucg
ccggccgaggugggaucccgaggccucuccaguccgccgagggcgcacca
ccggcccgucucgcccgccgcgccggggagguggagcacgagcgcacgug
uuaggacccgaaagauggugaacuaugccugggcagggcgaagccagagg
aaacucugguggagguccguagcgguccugacgugcaaaucggucguccg
accuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucc
cuccgaaguuucccucaggauagcuggcgcucucgcagacccgacgcacc
cccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuuggggc
cgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggc
ucgcuggcgugagccgggcguggaauggagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
gcaggacgguggccauggaagucggaauccgcuaaggaguguguaacaac
ucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgg
gcccauacccggccgucgccggcagucgagaguggacgggagcggcgggg
gcggcgcgcgcgcgcgcccgcccccggagccccgcggacgcuacgccgcg
acgaguaggagggccgcugcggugagccuugaagccuagggcgcgggccc
ggguggagccgccgcaggugcagaucuuggugguaguagcaaauauucaa
acgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcagu
ugaacaugggucagucgguccugagagaugggcgagcgccguuccgaagg
gacgggcgauggccuccguugcccucggccgaucgaaagggagucggguu
cagauccccgaauccggaguggcggagaugggcgccgcgaggcguccagu
gcgguaacgcgaccgaucccggagaagccggcgggagccccggggagagu
ucucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgag
agaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgguga
gcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgcc
gggccguacccauauccgcagcaggucuccaaggugaacagccucuggca
uguuggaacaauguagguaagggaagucggcaagccggauccguaacuuc
gggauaaggauuggcucuaagggcugggucggucgucggccggcgccuag
cagccgacuuagaacuggugcggaccaggggaauccgacuguuuaauuaa
aacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaugaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggaugaacgagauucccacugucccuacc
uacuauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcg
gggaaagaagacccuguugagcuugacucuagucuggcacggugaagaga
caugagagguguagaauaagugggaggcccccggcgcccccccggugucc
ccgcgaggggcccggggcgggguccgccggcccugcgggccgccggugaa
auaccacuacucugaucguuuuuucacugacccggugaggcgggggggcg
agccccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccgg
ccgggcgcgacccgcuccggggacagugccagguggggaguuugacuggg
gcgguacaccugucaaacgguaacgcagguguccuaaggcgagcucaggg
aggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuug
auuuucaguacgaauacagaccgugaaagcggggccucacgauccuucug
accuuuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaa
cuggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuuc
gaugucggcucuuccuaucauugugaagcagaauucaccaagcguuggau
uguucacccacuaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugauguguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauacggcagcgccgcggagcc
ucgguuggccucggauagccggucccccgccuguccccgccggcgccgcg
cgccgggaccgggguccggugcggagugcccuucguccugggaaacgggg
cgcggccggagaggcggccgcccccucgcccgucacgcaccggccguucg
uggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagucag
cccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zvk The Halastavi arva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.
• Resolution: 3.49 Å
• Binding residue (original residue number in PDB): R4 L5 T6 Y7 R8 R9 R10 L11 S12 Y13 N14 T15 K19 R21 R24 T25 P26 G27 R29 Y34 K37 K40 P42 A45 V48 R54 R60 P61 K62 M65 R66 S68 K69 T70 K72 V74 S75 Y78 G79 G80 S81 A84 K85 V87 R88 R90 I97 E98 K101 I102 V104
• Binding residue (residue number reindexed from 1): R3 L4 T5 Y6 R7 R8 R9 L10 S11 Y12 N13 T14 K18 R20 R23 T24 P25 G26 R28 Y33 K36 K39 P41 A44 V47 R53 R59 P60 K61 M64 R65 S67 K68 T69 K71 V73 S74 Y77 G78 G79 S80 A83 K84 V86 R87 R89 I96 E97 K100 I101 V103

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zvk, PDBe:6zvk, PDBj:6zvk
• PDBsum: 6zvk
• PubMed: 33296660
• UniProt: G1TXG5|RL34_RABIT Large ribosomal subunit protein eL34 (Gene Name=RPL34)