Structure of PDB 4v6x Chain CC Binding Site BS01

Receptor Information

>4v6x Chain CC (length=368) Species: 9606 (Homo sapiens)

ARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYA
VSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFA
PTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPLV
VEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQ
RRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWT
ESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQRALR
APRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDK
AAAAAAALQAKSDEKAAV

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): A4 R33 I36 F39 T42 N43 R45 K46 N47 N48 R49 Q50 Y52 V54 H60 Q61 T62 S63 S66 G70 A72 V73 A74 R75 I76 P77 R78 R80 G82 G83 T84 H85 R86 Q89 N94 M95 R97 R100 F102 A103 R109 R110 R114 N116 Q119 K120 R121 G141 R143 K163 T164 K172 W177 Y184 M189 R190 A191 G192 K193 K195 M196 R197 N198 R199 R201 R204 R205 N223 K234 P242 G243 H245 R268 K274 K294 A304 P305 R306 K307 K308 H310 R312 V313 K316 N321 L322 R323 I324 K333 N346 R350
• Binding residue (residue number reindexed from 1): A1 R30 I33 F36 T39 N40 R42 K43 N44 N45 R46 Q47 Y49 V51 H57 Q58 T59 S60 S63 G67 A69 V70 A71 R72 I73 P74 R75 R77 G79 G80 T81 H82 R83 Q86 N91 M92 R94 R97 F99 A100 R106 R107 R111 N113 Q116 K117 R118 G138 R140 K160 T161 K169 W174 Y181 M186 R187 A188 G189 K190 K192 M193 R194 N195 R196 R198 R201 R202 N220 K231 P239 G240 H242 R265 K271 K291 A301 P302 R303 K304 K305 H307 R309 V310 K313 N318 L319 R320 I321 K330 N343 R347

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• 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:4v6x, PDBe:4v6x, PDBj:4v6x
• PDBsum: 4v6x
• PubMed: 23636399
• UniProt: P36578|RL4_HUMAN Large ribosomal subunit protein uL4 (Gene Name=RPL4)