Structure of PDB 7pah Chain r Binding Site BS01

Receptor Information

>7pah Chain r (length=139) Species: 272634 (Mycoplasmoides pneumoniae M129)

MIAFAKQFRVRISPQKARLVCQLIVGKKTADAQNILSNTPKKAATLIAKL
LNSAIANATNNHGMNGDALYVFECVANQGPSMKRTIPRAKGSSNMITKRS
SNLVVKLSDNPNERQELIKQQKALVKKRVEGQQKAKMAR

Ligand information

>7pah 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: 7pah Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 9.5 Å
• Binding residue (original residue number in PDB): F4 A5 K6 F8 R11 Q15 K16 R18 K41 K42 K49 S53 A56 N57 N60 N61 E73 V75 A76 N77 Q78 G79 P80 R84 P87 R88 A89 K90 G91 S92 S93 N94 I96 K98 R99 N102 R114 Q121 L124 K126 K127 R128 G131 Q132
• Binding residue (residue number reindexed from 1): F4 A5 K6 F8 R11 Q15 K16 R18 K41 K42 K49 S53 A56 N57 N60 N61 E73 V75 A76 N77 Q78 G79 P80 R84 P87 R88 A89 K90 G91 S92 S93 N94 I96 K98 R99 N102 R114 Q121 L124 K126 K127 R128 G131 Q132

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0046677 response to antibiotic

Cellular Component

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

External links

• PDB: RCSB:7pah, PDBe:7pah, PDBj:7pah
• PDBsum: 7pah
• PubMed: 36171285
• UniProt: P75575|RL22_MYCPN Large ribosomal subunit protein uL22 (Gene Name=rplV)