Structure of PDB 6y6x Chain Lf Binding Site BS01

Receptor Information

>6y6x Chain Lf (length=109) Species: 9606 (Homo sapiens)

SGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVY
KAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRI
RVMLYPSRI

Ligand information

>6y6x Chain L5 (length=3773)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggucggucgcggccggcgccuagcagccgacuuagaacugg
ugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaagg
cccgcggcggguguugacgcgaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaug
acucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaug
aauggaugaacgagauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguu
gagcuugacucuagucuggcacggugaagagacaugagagguguagaaua
agugggaggcccccggcgcccccccgguguccccgcgaggggcccggggc
gggguccgccggcccugcgggccgccggugaaauaccacuacucugaucg
uuuuuucacugacccggugaggcgggggggcgagccccgaggggcucucg
cuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcucc
ggggacagugccagguggggaguuugacuggggcgguacaccugucaaac
gguaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgu
ggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauaca
gaccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagc
aggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaa
gcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuau
cauugugaagcagaauucaccaagcguuggauuguucacccacuaauagg
gaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugauguguuguugccaugguaauccugcucaguacgagaggaaccgc
agguucagacauuugguguaugugcuuggcugaggagccaauggggcgaa
gcuaccaucugugggauuaugacugaacgccucuaagucagaaucccgcc
caggcggaacgauacggcagcgccgcggagccucgguuggccucggauag
ccggucccccgccgggguccggugcggagugcccuucguccugggaaacg
gggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacgu
ucguggggaaccuggcgcuaaaccauucguagacgaccugcuucuggguc
gggguuucguacguagcagagcagcucccucgcugcgaucuauugaaagu
cagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y6x Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): S2 G3 R4 W6 K8 K15 R16 G17 L18 R19 N20 Q21 R22 E23 H24 K29 Y34 R36 L43 Y51 K52 K54 N55 T57 V58 P60 T67 R68 V69 W71 K73 R76 H78 G79 N80 S81 R85 K87 R89 S90 N91 P93 A94 R100 R102 R109
• Binding residue (residue number reindexed from 1): S1 G2 R3 W5 K7 K14 R15 G16 L17 R18 N19 Q20 R21 E22 H23 K28 Y33 R35 L42 Y50 K51 K53 N54 T56 V57 P59 T66 R67 V68 W70 K72 R75 H77 G78 N79 S80 R84 K86 R88 S89 N90 P92 A93 R99 R101 R108

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6y6x, PDBe:6y6x, PDBj:6y6x
• PDBsum: 6y6x
• PubMed: 32601485
• UniProt: P18077|RL35A_HUMAN Large ribosomal subunit protein eL33 (Gene Name=RPL35A)