Structure of PDB 7pio Chain i Binding Site BS01

Receptor Information

>7pio Chain i (length=144) Species: 272634 (Mycoplasmoides pneumoniae M129)

KTSMLTKEQANKRRQWYIVDAAGLVLGKLAVKAADLIRGKNKVDFTPNQD
CGDYLIIINSDQVVLTGNKKENEFWYHHSQYIGGIKKVSGRDMLKKQSDK
LVYNAVKGMLPDNRLSRRWITKVHVFKGDKHNMEAQKPTTLNWS

Ligand information

>7pio Chain 3 (length=2878)

aguuacuaagggcuuaugguggaugccuuggcacuaauaggcgaugaagg
acguguuaaccugcgauaagcuucggguaggugguaagaaccucagaucc
ggagauuuccgaauggagcaauccgguaguuggaaacagcuaucauuaau
ugaugaauaaauagucaauuaaagcaauacguggugaagugaaacaucuc
aguagccacaggaaaagaaaacgaaugugauuccguguguaguggcgagc
gaaagcggaacaggccaaacuuaucauuagauagggguuguagggcuugc
aauguggacuugaaaacgauagaagaagcuguuggaaagcagcgcgcaaa
agggugauagccccguauuugaaauuguuuucauaccuagcgagaucccu
gaguagcucggaaaacguuauuuugagugaaucugcccagaccauugggu
aagccuaaauacuaauuagugaccgauagcgaaacaguaccgugagggaa
aggugaaaagaacccagagaugggagugaaauagauucugaaaccauaug
ccuacaacgugucagagcacauuaaugugugauggcgugcguuuugaagu
augagccggcgaguuaugauagcaagcguuaguuaaccaggagaugggga
gcuguagcgaaagcgaguuuuaaaagagcguuuguuuguuauuauagacc
cgaaacggguugagcuagucaugagcagguugaagguugaguaacaucaa
cuggaggaccgaaccgacucucguugaaacgauagcggaugacuugugau
uaggggugaaauuccaaucgaaauccgugauagcugguucucgucgaaau
agcuuuaaggcuagcgugagaucacaaauaaguggagguaaagcuacuga
auguaugauggcgccggcguacugaauacaauuaaacucugaaugccauu
uauuuuauucucgcagucagacagugggggauaagcuucauugucaagag
gggaagagcccagaucauuaaauaagguccccaaaauauacuaaguggaa
aaggaugugaaagugcuaaaacagcaaggauguuggcuuagaagcagcca
ucguuuaaagagugcguaacagcucacuugucgaguguuuuugcgccgaa
gauguaacggggcuaaguauauuaccgaauuuauggauaagauuuauauc
uugugguagacgagcguuguauuggaguugaagucaaagcgugagcauug
guggauccaauacaagugagaaugccggcaugaguaacgcuugggaguga
gaaucucccaaaccgauugacuaagguuuccuggaccagggucguccuuc
caggguuagucuggaccuaagcugaggcugaaaagcguaggcgauggaca
acagguuaauauuccuguacuuacaguuagacugauggagugacaaagaa
gguuuuccacccccauaauuggauuuggggauaaaucauaaggugguaca
auaggcaaauccguugugcauaacauugagugaugaugucgagugaaagu
agcgaaggugguauuaaucaugcuuucaagaaaagcuucuaggguuaauc
uagcuguaaccaguaccgagaacgaacacacguagucaaggagaggaucc
uaagguuagcgagugaacuauagccaaggaacucugcaaauuaaccccgu
aaguuagcgagaaggggugcuuauguaaaaguaagccgcagugaagaacg
aggggggacuguuuaacuaaaacacaacucuaugccaaaccguaagguga
uguauauggggugacaccugcccagugcuggaagguuaaagaaggagguu
agcgcaagcgaagcuuuuaacugaagccccagugaacggcggccguaacu
auaacgguccuaagguagcgaaauuccuagucggguaaauuccgucccgc
uugaaugguguaaccaucucuugacugucucggcuauagacucggugaaa
uccagguacgggugaagacacccguuaggcgcaacgggacggaaagaccc
cgugaagcuuuacuguagcuuaauauugaucaggacauuaucauguagag
aauagguaggagcaaucgaugcaaguucgcuaggacuuguugaugcgaaa
gguggaauacuacccuugguugugugcuguucuaauugguaacuguuauc
caguuucaagacaguguuaggugggcaguuugacuggggcggucgccucc
uaaaagguaacggaggcguacaaagguaccuucaguacgguuggaaaucg
uauguagaguguaaugguguaagggugcuugacugugagacauacagguc
gaacaggugagaaaucaggucauagugauccggugguccaguauggaaug
gccaucgcucaacggauaaaagcuacuccggggauaacaggcugauacug
cccaagaguucauaucgacggcaguguuuggcaccucgaugucgacucau
cucauccucgagcugaagcagguucgaaggguucggcuguucgccgauua
aagagauacgugaguuggguucaaaccgucgugagacagguuggucccua
ucuauugugcccguaggaagauugaagaguguugcuucuaguacgagagg
accgaagcgaggacaccucuuaugcuccaguuguagcgccagcugcaccg
cuggguaguaacgugucuauuagauaaacgcugaaagcaucuaaguguga
aacuaucucaaagauuaaucuucccauuucgcaagaaaguaagagccguc
aaagacgaugacguugauagguuacagguguaagcauagugauauguuga
gcugaguaauacuaauugcucgaggacu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7pio Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 9.5 Å
• Binding residue (original residue number in PDB): K3 T4 K9 Q11 A12 K42 P49 N50 Q51 T68 K71 E75 W77 Y78 H80 Y83 I84 I87 K88 K102 A107 G110 M111 P113 N115 R116 R119 R120 T123 Q138
• Binding residue (residue number reindexed from 1): K1 T2 K7 Q9 A10 K40 P47 N48 Q49 T66 K69 E73 W75 Y76 H78 Y81 I82 I85 K86 K100 A105 G108 M109 P111 N113 R114 R117 R118 T121 Q136

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pio, PDBe:7pio, PDBj:7pio
• PDBsum: 7pio
• PubMed: 36171285
• UniProt: P75178|RL13_MYCPN Large ribosomal subunit protein uL13 (Gene Name=rplM)