Structure of PDB 7mdz Chain S Binding Site BS01

Receptor Information

>7mdz Chain S (length=176) Species: 9986 (Oryctolagus cuniculus)

MKASGTLREYKVVGRCLPTPKCRTPPLYRMRIFAPNHVVAKSRFWYFVSQ
LKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDL
TTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKI
KFPLPHRVLRRQHKPRFTTKRPNTFF

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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....>>>>.....((......<<<.....))>>>...>.>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...(((((..<<<<<<)))))..]]]........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<<....<<<<<<<.<<<<..<<<<<<<
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>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<<<
<<<...<<..<<<..<<<<<<<......<<<<<<<<.>>>>>>>>.....
..>>>>>>>..>>>.........>>>>>>..>>>>>>>>>>>.....<<.
......>>.........<...<<<<<<..>>>>>>...<.<<..<<<.<<
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>>>>>.>>>...>>>>>.>................>.........>>.>>
>>>....>>>>...>>>>>>>>..<<<<........>>>><<<<<<....
<<<<<<<<<<<<<..<<<...<<<<.....>>>>.....>>>...<<...
.>>...<<<<<<<<<<..>>>>>>>>>>..<<<<<...<<<..<<<....
[[.[[.>>>..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>
>>>>>.>>....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<
<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<..<<.
<<........>>>>.>>>....>>>>>>>>>...<<.......>>.....
.>>>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<.<<<<
<<<...<<<.<<<<<<<<<...<<<....<<<....<<<..<<<<<<...
......>>>>>>>>>....>>>..>.>>...>>>>>>>...<<<<<<<<<
.<......>>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<
.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((
.......<<<<<......<..........<<<.<<<<<<<<<<.......
<<<<<.<<.....................>>.........<<......>>
...>>>>>...>>>>>>>>>>>>>..........))).>....>>>>>..
>>>...>>>>>>><<<<<<.<<<....................]].]]..
...........>>>>>>>>>....>>>>>>...<<<<<<<<.<<......
<<<<.<<<<....>>>>>>>>...>>>>>>>>>>........>>>>>><<
.....<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<<..
.<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<
....>>>..........<<.<<<<<<<<<...>>>>>>>>>>>......>
>....>>>..<<<<<........>>>>>))<<<<....<<<<<...<<<<
<<<....>>>>>>>...<<<....>>>...<..<<<<<<<...<<<<<<<
<<<<<.<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<..
...<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<....
...>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>>..>..
........>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<
<<.....>>>>..>>>....<<<<.....<<<<<<<.<<.........<.
....<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.>>>>>.
.>>>>>>.>>............<<<<<<<<<..<<<.........>>>..
<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<<<..<
<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>><
<<<<<.......>>>>>>........<...........<<<<<.......
>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>
>>>>>....>>....<<<<<........>>>>>....[[[[[..{{{.{{
......[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<..>>>>>
>>>...<<<<<.....<<<<..<<.<.<<<>>.>>.>>............
..<<<<<<<<<..>>>>>>>>>..>>>>..>>>>>....>>>>>>>>>..
>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<..
.<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>....>
>>>>>>...<<<.<<<<<.......>>>>.>>>><<<<....>>>>>>))
)]......((((((..(((..>>>>>>.)))))))))..........]]]
]..}}]]]].......<<.<...<<<<<<...<<.......>>...>>>>
>>....>.>.>.......<<<<<.<<<<<<..<.<.<<<<<......>>>
>>...>.>.<<<.........>>>.....>>>>>..>...>>>.>>....
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.<<<<<...........>>>>>....>>>>.>>>...>.>>>>>>.<<<<
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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): K2 A3 S4 G5 R23 Y63 Q66 V67 F68 E69 K70 S86 R87 S88 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 A134 R139 H146 D147 S148 P155 H156 R157 V158 R160 R161 H163 R166 T169 K170 R171 P172 N173 T174 F175 F176
• Binding residue (residue number reindexed from 1): K2 A3 S4 G5 R23 Y63 Q66 V67 F68 E69 K70 S86 R87 S88 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 A134 R139 H146 D147 S148 P155 H156 R157 V158 R160 R161 H163 R166 T169 K170 R171 P172 N173 T174 F175 F176

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:7mdz, PDBe:7mdz, PDBj:7mdz
• PDBsum: 7mdz
• PubMed: 34403584
• UniProt: G1TTY7|RL18A_RABIT Large ribosomal subunit protein eL20 (Gene Name=RPL18A)