Structure of PDB 7pir Chain g Binding Site BS01

Receptor Information

>7pir Chain g (length=122) Species: 272634 (Mycoplasmoides pneumoniae M129)

AKKDKAQQVADVSHLLSTSAGFVIFDYTSMSAIEATSIRKKLFKNGSKIK
VIKNNILRRALKAGKFEGIDETAIKGKLAVAVGVNEIVETLKAVDGVVKA
KEAMNFVCGRAFNSADLEKIAK

Ligand information

>7pir 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: 7pir Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 12.1 Å
• Binding residue (original residue number in PDB): A3 K4 K5 S31 M32 S33 A34 I35 R41 K50 I51 K52 V53 I54 K55 N56 N57 R60 R61 A75 I76 G78 K79 L80
• Binding residue (residue number reindexed from 1): A1 K2 K3 S29 M30 S31 A32 I33 R39 K48 I49 K50 V51 I52 K53 N54 N55 R58 R59 A73 I74 G76 K77 L78

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pir, PDBe:7pir, PDBj:7pir
• PDBsum: 7pir
• PubMed: 36171285
• UniProt: P75240|RL10_MYCPN Large ribosomal subunit protein uL10 (Gene Name=rplJ)