Structure of PDB 4v6x Chain Cb Binding Site BS01

Receptor Information

>4v6x Chain Cb (length=78) Species: 9606 (Homo sapiens)

AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNK
KGLKKMQANNAKAMSARAEAIKALVKPK

Ligand information

>4v6x Chain A5 (length=4298)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgccccccguuccucccgaccccuccacccgccc
ucccuucccccgccgccccgggcuccggcgggugcgggggugggcgggcg
gggccggggguggggucggcgggggaccgucccccgaccggcgaccggcc
gccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggga
cggcugggaaggcccggcggggaagguggcucggggggccccguccgucc
guccggcggcggcggcggcggcgggaccgaaaccccccccgaguguuaca
gcccccccggcagcagcacucgccgaaucccggggccgagggagcgagac
ccgucgccgcgcucuccccccucccggcgcccacccccgcggggacuccc
ccgcgggggcgcgccggcgucuccucgugggggggccgggccaccccucc
cacggcgcgaccgcucucccaccccuccuccccgcgcccccggggugccg
cgcgcgggucggggggcggggcggacuguccccagugcgccccgggcggg
ucgcgccgucgggcccgggggagguucucucggggccacgcgcgcguccc
ccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucgg
cuacccacccgacccgucuugaaacacggaccaaggagucuaacacgugc
gcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaagg
ccggcgcgcucgccggccgaggugggaucccgaggccucuccaguccgcc
gagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagca
cgagcgcacguguuaggacccgaaagauggugaacuaugccugggcaggg
cgaagccagaggaaacucugguggagguccguagcgguccugacgugcaa
aucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucua
guagcugguucccuccgaaguuucccucaggauagcuggcgcucucgcag
acccgacgcacccccgccacgcaguuuuauccgguaaagcgaaugauuag
aggucuuggggccgaaacgaucucaaccuauucucaaacuuuaaaugggu
aagaagcccggcucgcuggcguggagccgggcguggaaugcgagugccua
gugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgc
cggguuaaggcgcccgaugccgacgcucaucagaccccagaaaagguguu
gguugauauagacagcaggacgguggccauggaagucggaauccgcuaag
gaguguguaacaacucaccugccgaaucaacuagcccugaaaauggaugg
cgcuggagcgucgggcccauacccggccgucgccggcagucgagagugga
cgggagcggcgggggcggcgcgcgcgcgcgcgcguguggugugcgucgga
gggcggccuccucccgcccacgccccgcuccccgcccccggagccccgcg
gacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagcc
uagggcgcgggcccggguggagccgccgcaggugcagaucuuggugguag
uagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguucc
augugaacagcaguugaacaugggucagucgguccugagagaugggcgag
cgccguuccgaagggacgggcgauggccuccguugcccucggccgaucga
aagggagucggguucagauccccgaauccggaguggcggagaugggcgcc
gcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcggga
gccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaau
ggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccg
gcggcguccggugagcucucgcuggcccuugaaaauccgggggagagggu
guaaaucucgcgccgggccguacccauauccgcagcaggucuccaaggug
aacagccucuggcauguuggaacaauguagguaagggaagucggcaagcc
ggauccguaacuucgggauaaggauuggcucuaagggcugggucggucgg
gcuggggcgcgaagcggggcugggcgcgcgccgcggcuggaucuggacgc
gagccgggcccuucccguggaucgccccagcugcggcgggcgucgcggcc
gcgcgguuccgcgcggcgccucgccucggccggcgccuagcagccgacuu
agaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcau
cgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggaugaacgagauucccacugucccuaccuacuauccag
cgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaagagacaugagaggu
guagaauaagugggaggcccccggcgcccccccgguguccccgcgagggg
cccggggcgggguccgccggcccugcgggccgccggugaaauaccacuac
ucugaucguuuuuucacugacccggugaggcgggggggcgagccccgagg
ggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcga
cccgcuccggggacagugccagguggggaguuugacuggggcgguacacc
ugucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaa
ccucccguggagcagaagggcaaaagcucgcuugaucuugauuuucagua
cgaauacagaccgugaaagcggggccucacgauccuucugaccuuuuggg
uuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugug
gcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcu
cuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugauguguuguugccaugguaauccugcucaguacgaga
ggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaau
ggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucaga
aucccgcccaggcggaacgauacggcagcgccgcggagccucgguuggcc
ucggauagccggucccccgccuguccccgccggcgggccgcccccccccu
ccacgggagggcgcgugccccgccgcgcgccgggaccgggguccggugcg
gagugcccuucguccugggaaacggggcgcggccggagaggcggccgccc
ccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccau
ucguagacgaccugcuucugggucgggguuucguacguagcagagcagcu
cccucgcugcgaucuauugaaagucagcccucgacacaaggguuuguc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6x Structures of the human and Drosophila 80S ribosome.
• Resolution: 5.0 Å
• Binding residue (original residue number in PDB): K3 S4 K5 N6 H7 T9 H10 N11 Q12 R14 K15 R18 K23 R25 S26 R28 Y29 K33 D36 P37 K38 F39 N42 M43 R44 F45 A46 K47 H49 N50 K52 L54 K56 Q58 N61 M65
• Binding residue (residue number reindexed from 1): K2 S3 K4 N5 H6 T8 H9 N10 Q11 R13 K14 R17 K22 R24 S25 R27 Y28 K32 D35 P36 K37 F38 N41 M42 R43 F44 A45 K46 H48 N49 K51 L53 K55 Q57 N60 M64

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008201 heparin binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0007566 embryo implantation

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6x, PDBe:4v6x, PDBj:4v6x
• PDBsum: 4v6x
• PubMed: 23636399
• UniProt: P47914|RL29_HUMAN Large ribosomal subunit protein eL29 (Gene Name=RPL29)