Structure of PDB 3j7r Chain b Binding Site BS01

Receptor Information

>3j7r Chain b (length=75) Species: 9823 (Sus scrofa)

AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNK
KGLKKMQANNAKAMSARAEAIKALV

Ligand information

>3j7r Chain 5 (length=3720)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucggccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccucccggcgccgccggggggggccgggccaccc
cucccacggcgcgaccgcucggggcggacuguccccagugcgccccgggc
gggucgcgccgucgggcccgggggaggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcacacgcag
uuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucuc
aaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcguga
gccgggcguggaauggagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagcggcgggggcggcgcgcgcg
cgcgcccgcccccggagccccgcggacgcuacgccgcgacgaguaggagg
gccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgc
cgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuug
aaggccgaaguggagaaggguuccaugugaacagcaguugaacauggguc
agucgguccugagagaugggcgagcgccguuccgaagggacgggcgaugg
ccuccguugcccucggccgaucgaaagggagucggguucagauccccgaa
uccggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcga
ccgaucccggagaagccggcgggagccccggggagaguucucuuuucuuu
gugaagggcagggcgcccuggaauggguucgccccgagagaggggcccgu
gccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggc
ccuugaaaauccgggggagaggguguaaaucucgcgccgggccguaccca
uauccgcagcaggucuccaaggugaacagccucuggcauguuggaacaau
guagguaagggaagucggcaagccggauccguaacuucgggauaaggauu
ggcucuaagggcugggucggucgucggccggcgccuagcagccgacuuag
aacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucg
cgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggaugaacgagauucccacugucccuaccuacuauccagcg
aaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaagac
ccuguugagcuugacucuagucuggcacggugaagagacaugagaggugu
agaauaagugggaggcccgggccgccggugaaauaccacuacucugaucg
uuuuuucacugacccggugaggcgggggggcgagccccgaggggcucucg
cuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcucc
ggggacagugccagguggggaguuugacuggggcgguacaccugucaaac
gguaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgu
ggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauaca
gaccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagc
aggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaa
gcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuau
cauugugaagcagaauucaccaagcguuggauuguucacccacuaauagg
gaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugauguguuguugccaugguaauccugcucaguacgagaggaaccgc
agguucagacauuugguguaugugcuuggcugaggagccaauggggcgaa
gcuaccaucugugggauuaugacugaacgccucuaagucagaaucccgcc
caggcggaacgauacggcagcgccgcggagccucgguuggccucggauag
ccggucccccgcgggguccggugcggagugcccuucguccugggaaacgg
ggcgcggccggagaggcggccgcccccucgcccgucacgcacgccguucg
uggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagucag
cccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j7r Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): K3 S4 K5 N6 H7 T8 T9 H10 N11 Q12 S13 R14 K15 H17 R18 K22 K23 S26 Q27 R28 Y29 S31 L32 K33 D36 P37 K38 F39 R41 N42 M43 R44 F45 A46 K47 H49 N50 K52 M57 N60 N61 M65 R68
• Binding residue (residue number reindexed from 1): K2 S3 K4 N5 H6 T7 T8 H9 N10 Q11 S12 R13 K14 H16 R17 K21 K22 S25 Q26 R27 Y28 S30 L31 K32 D35 P36 K37 F38 R40 N41 M42 R43 F44 A45 K46 H48 N49 K51 M56 N59 N60 M64 R67

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0098556 cytoplasmic side of rough endoplasmic reticulum membrane
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j7r, PDBe:3j7r, PDBj:3j7r
• PDBsum: 3j7r
• PubMed: 24930395
• UniProt: Q95281|RL29_PIG Large ribosomal subunit protein eL29 (Gene Name=RPL29)