Structure of PDB 5o60 Chain E Binding Site BS01

Receptor Information

>5o60 Chain E (length=209) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

TLKVDVKTPAGKTDGSVELPAELFDVEPNIALMHQVVTAQLAAKRQGTHS
TKTRGEVSGGGKKPYRQKGTGRARQGSTRAPQFTGGGTVHGPKPRDYSQR
TPKKMIAAALRGALSDRARNDRIHAVTELVEGQTPSTKSAKTFLGTLTEN
KKVLVVIGRTDEVGAKSVRNLPGVHVISPDQLNTYDVLNADDVVFSVEAL
NAYISANSK

Ligand information

>5o60 Chain A (length=3119)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaaccaggagguuggcuuagaagcagccacccuug
aaagagugcguaauagcucacuggucaagugauugugcgccgauaaugua
gcggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugg
guaggggagcguccugcauccggugaagccgccgagugaucgaguggugg
agggugugggagugagaaugcaggcaugaguagcgauuaggcaagugaga
accuugcccgccgaaagaccaaggguuccugggccaggccaguccgccca
gggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaac
ggguugauauucccguacccguguaugugcguccaugaugaaucagcggu
acuaaccauccaaaaccaccgugaccgcaccuuucgggguguggcguugg
uggggcugcaugggaccuucguugguaguagucaagcgauggggugacgc
aggaagguagccguaccggucagugguaauaccgggguaagccuguaggg
agucagauagguaaauccgucuggcauauauccugagaggugaugcauag
ccgagugaggcgaauucggugauccuaugcugccgagaaaagccucuagc
gaggacauacacggcccguaccccaaaccaacacagguggucagguagag
aauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaaugcc
cccguaacuucgggagaagggggacccacauggcguguaagccuuuacgg
cccaagcgugaguggguggcacaaaccagugagaagcgacuguuuacuaa
aaacacagguccgugcgaagucgcaagacgauguauacggacugacgccu
gcccggugcuggaagguuaagaggacccguuaacucccuuugggggugaa
gcggagaauuuaagccccaguaaacggcggugguaacuauaaccauccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaauggcgua
acgacuucucaacugucucaaccauagacucggcgaaauugcacuacgag
uaaagaugcucguuacgcgcggcaggacgaaaagaccccgggaccuucac
uacaacuugguauuggugcucgauacgguuuguguaggauaggugggaga
cugugaagcucacacgccaguguggguggagucguuguugaaauaccacu
cugaucguauugggccucuaaccucggaccguauauccgguucagggaca
gugccugguggguaguuuaacuggggcgguugccuccuaaaauguaacgg
aggcgcccaaagguucccucaaccuggacggcaaucagguguugagugua
agugcacaagggagcuugacugcgagacggacaugucgagcagggacgaa
agucgggacuagugauccggcaccucugaguggaaggggugucgcucaac
ggauaaaagguaccccggggauaacaggcugaucuuccccaagaguccau
aucgacgggaugguuuggcaccucgaugucggcucgucgcauccuggggc
uggagcaggucccaaggguugggcuguucgcccauuaaagcggcacgcga
gcuggguuuagaacgucgugagacaguucggucucuauccgccgcgcgcg
ucagaagcuugaggaaaccugucccuaguacgagaggaccgggacggacg
aaccucugguauaccaguugucccaccaggggcacggcuggauagccacg
uucggacaggauaaccgcugaaagcaucuaagcgggaaaccucuuccaag
accaggcuucucacccucuaggagggauaaggccccccgcagaccacggg
auugauagaccagaccuggaagccuaguaauaggugcagggaacuggcac
uaaccggccgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5o60 The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
• Resolution: 3.18 Å
• Binding residue (original residue number in PDB): N30 L33 H35 Q36 Q41 L42 K45 R46 Q47 T49 H50 K53 T54 R55 G56 V58 S59 G60 K64 Q68 K69 G70 G72 R73 R75 Q76 G77 R80 P82 Q83 F84 T85 G86 T89 V90 H91 P93 R96 Q100 R101 P103 K104 K105 M106 T138 K139 K142 K153 R160 K167 R170 N171 H176 D181 Q182 N184 Y186 D187 N190
• Binding residue (residue number reindexed from 1): N29 L32 H34 Q35 Q40 L41 K44 R45 Q46 T48 H49 K52 T53 R54 G55 V57 S58 G59 K63 Q67 K68 G69 G71 R72 R74 Q75 G76 R79 P81 Q82 F83 T84 G85 T88 V89 H90 P92 R95 Q99 R100 P102 K103 K104 M105 T137 K138 K141 K152 R159 K166 R169 N170 H175 D180 Q181 N183 Y185 D186 N189

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5o60, PDBe:5o60, PDBj:5o60
• PDBsum: 5o60
• PubMed: 28683309
• UniProt: A0QSD2|RL4_MYCS2 Large ribosomal subunit protein uL4 (Gene Name=rplD)