Structure of PDB 7pam Chain t Binding Site BS01

Receptor Information

>7pam Chain t (length=111) Species: 272634 (Mycoplasmoides pneumoniae M129)

MQRIKKGDKVVVITGKNKGGSGIVLKIMPARQQAIVEGLNKVTRHKKKDQ
TTKRAAKQSTGKVQQEAPIFLSKLALFDQKAKQQTIGKIKYVMDPKTNKK
TRVFKKSNNTL

Ligand information

>7pam 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: 7pam Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 6.8 Å
• Binding residue (original residue number in PDB): M1 Q2 R3 K6 T14 G15 K16 K18 R44 H45 K46 K47 D49 T60 F70 S72 K73 K88 Y91 V92 K100 K105 K106
• Binding residue (residue number reindexed from 1): M1 Q2 R3 K6 T14 G15 K16 K18 R44 H45 K46 K47 D49 T60 F70 S72 K73 K88 Y91 V92 K100 K105 K106

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:7pam, PDBe:7pam, PDBj:7pam
• PDBsum: 7pam
• PubMed: 36171285
• UniProt: Q50307|RL24_MYCPN Large ribosomal subunit protein uL24 (Gene Name=rplX)