Structure of PDB 7mdz Chain W Binding Site BS01

Receptor Information

>7mdz Chain W (length=63) Species: 9986 (Oryctolagus cuniculus)

MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQIN
WTVLYRRKHKKGQ

Ligand information

>7mdz Chain 5 (length=3541)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugcgccgcgcucuccccccucgggggggccgggccaccccucc
cacggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgc
gccgucgggcccggggggccacgcgucccccgcgagcgcacggggucggc
ggcgaugucggcuacccacccgacccgucuugaaacacggaccaaggagu
cuaacacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaa
ggugaaggccggcggcgcgccgccggccgaggugggaucccgaggccuuc
caguccgccgagggcgcaccaccggcccgucucgcccgccgcgccgggga
gguggagcacgagcgcacguguuaggacccgaaagauggugaacuaugcc
ugggcagggcgaagccagaggaaacucugguggagguccguagcgguccu
gacgugcgaaucggucguccgaccuggguauaggggcgaaagacuaaucg
aaccaucuaguagcugguucccuccaaaguuucccucaggauagcuggcg
cucuccgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccg
aaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggcuc
gcugguguggagccgggcguggaaugcgagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
gcaggaugguggccauggaagucggaauccgcuaaggaguguguaacaac
ucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgg
gcccauacccggccgucgcuggcagucggcagagcgagaaagagaguggc
gcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaa
gccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggugg
uaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaagggu
uccaugugaacagcaguugaacaugggucagucgguccugagagaugggc
gagcgccguuccgaagggacgggcgauggccuccguugcccucagccgau
cgaaagggagucggguucagauccccgaauccggaguggcggagaugggc
gccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcg
ggagccccggggagaguucucuuuucuuugugaagggcagggcgcccugg
aauggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguu
ccggcggcguccggugagcucucgcuggcccuugaaaauccgggggagag
gguguaaaucucgcgccgggccguacccauauccgcagcaggucuccaag
gugaacagccucuggcauguuggaacaauguagguaagggaagucggcaa
gccggauccguaacuucgggauaaggauuggcucuaagggcuggcagccg
acuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaa
gcaucgcgaaggcccgcggcggguguugacgcgaugugauuucugcccag
ugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcg
ggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauua
gugacgcgcaugaauggaugaacgagauucccacugucccuaccuacuau
ccagcgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaa
gaagacccuguugagcuugacucuagucuggcacggugaagagauuuuuu
cacugacccggugaggcgggggggcgagccgggcucucgcuucuggcgcc
aagcgcccggccggccgggcgcgacccgcuccggggacagugccaggugg
ggaguuugacuggggcgguacaccugucaaacgguaacgcagguguccua
aggcgagcucagggaggacagaaaccucccguggagcagaagggcaaaag
cucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggcc
ucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaagu
uaccacagggauaacuggcuuguggcggccaagcguucauagcgacgucg
cuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaauuc
accaagcguuggauuguucacccacuaauagggaacgugagcuggguuua
gaccgucgugagacagguuaguuuuacccuacugaugauguguuguugcc
augguaauccugcucaguacgagaggaaccgcagguucagacauuuggug
uaugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauu
augacugaacgccucuaagucagaaucccgcccaggcggaacgauagcgc
cggagccucgguuggccucggauagccggucccccgccgggguccggugc
ggagagcccuucgucccgggaaacggggcggccggaaagggggccgcccu
cucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauu
cguagacgaccugcuucugggucgggguuucguacguagcagagcagcug
cugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mdz Discovery of C13-Aminobenzoyl Cycloheximide Derivatives that Potently Inhibit Translation Elongation.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): G16 R19 K35 R44 Q48 N50 W51 R56 K61
• Binding residue (residue number reindexed from 1): G16 R19 K35 R44 Q48 N50 W51 R56 K61

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0010458 exit from mitosis
• GO:0021554 optic nerve development
• GO:0031290 retinal ganglion cell axon guidance
• GO:0060041 retina development in camera-type eye

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7mdz, PDBe:7mdz, PDBj:7mdz
• PDBsum: 7mdz
• PubMed: 34403584
• UniProt: G1SE28|RL24_RABIT Large ribosomal subunit protein eL24 (Gene Name=RPL24)