Structure of PDB 7pas Chain n Binding Site BS01

Receptor Information

>7pas Chain n (length=112) Species: 272634 (Mycoplasmoides pneumoniae M129)

MKTRTEQRRLRHKRIVKKIRATNHDNRVVLMVIKSLNHISVQAWDFSQNI
VLASSSSLALKLKNNAKLVGQDIADKLVKLKLTNVVFDTGGSKYHGRIAA
LAEAARERGLNF

Ligand information

>7pas 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: 7pas Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 16.0 Å
• Binding residue (original residue number in PDB): M1 Q7 L10 R11 R14 I15 K17 K18 T22 N23 R27 F91 T93 K97 Y98 R110 F116
• Binding residue (residue number reindexed from 1): M1 Q7 L10 R11 R14 I15 K17 K18 T22 N23 R27 F87 T89 K93 Y94 R106 F112

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:7pas, PDBe:7pas, PDBj:7pas
• PDBsum: 7pas
• PubMed: 36171285
• UniProt: Q50302|RL18_MYCPN Large ribosomal subunit protein uL18 (Gene Name=rplR)