Structure of PDB 7pal Chain C Binding Site BS01

Receptor Information

>7pal Chain C (length=203) Species: 272634 (Mycoplasmoides pneumoniae M129)

MKYTGSIFKRSRRLGFSLLENNKEFSKGKKRKTIPGQHGNRFRSSTMSGY
AQQLQEKQRMQYMYGITDKQFRRLFRLVLKQRGNLAVNLFRVLESRLDNI
VYRMGFAPTRRSARQLVNHGHVLLNDRTVDTPSIILNPGDKVRLKAKTIK
IPIVKAASESGVVSPFVETNNKTFEGTYVRFPERSELPAGINESYVVEWY
KRL

Ligand information

>7pal Chain 5 (length=1493)

ucugagaguuugauccuggcucaggauuaacgcuggcggcaugccuaaua
caugcaagucgaucgaaaguaguaauacuuuagaggcgaacgggugagua
acacguauccaaucuaccuuauaaugggggauaacuaguugaaagacuag
cuaauaccgcauaagaacuuugguucgaaucaaaguugaaaggaccugca
aggguucguuauuugaugagggugcgccauaucagcuaguugguggggua
acggccuaccaaggcaaugacguguagcuaugcugagaaguagaauagcc
acaaugggacugagacacggcccauacuccuacgggaggcagcaguaggg
aauuuuucacaaugagcgaaagcuugauggagcaaugccgcgugaacgau
gaaggucuuuaagauuguaaaguucuuuuauuugggaagaaugacuuuag
cagguaauggcuagaguuugacuguaccauuuugaauaagugacgacuaa
cuaugugccagcagucgcgguaauacauaggucgcaagcguuauccggau
uuauugggcguaaagcaagcgcaggcggauugaaaagucugguguuaaag
gcagcugcuuaacaguuguaugcauuggaaacuauuaaucuagagugugg
uagggaguuuuggaauuucauguggagcggugaaaugcguagauauauga
aggaacaccaguggcgaaggcgaaaacuuaggccauuacugacgcuuagg
cuugaaaguguggggagcaaauaggauuagauacccuaguaguccacacc
guaaacgauagauacuagcugucggggcgauccccucgguagugaaguua
acacauuaaguaucucgccuggguaguacauucgcaagaaugaaacucaa
acggaauugacggggacccgcacaagugguggagcauguugcuuaauucg
acgguacacgaaaaaccuuaccuagacuugacauccuuggcaaaguuaug
gaaacauaaugccgagugacagguggugcaugguugucgucagcucgugu
cgugagauguuggguuaagucccgcaacgagcgcaacccuuaucguuagu
uacauugucuagcgagacugcuaaugcaaauuggaggaaggaagggauga
cgucaaaucaucaugccccuuaugucuagggcugcaaacgugcuacaaug
gccaauacaaacagucgccagcuuguaaaagugagcaaaucuguaaaguu
ggucucaguucggauugagggcugcaauucguccucaugaagucggaauc
acuaguaaucgcgaaucagcuaugucgcggugaauacguucucgggucuu
guacacaccgcccgucaaacuaugaaagcugguaauauuuaaaaacgugu
ugcuaaccauuaggaagcgcaugucaaggauagcaccggugauuggaguu
aagucguaacaagguaccccuacgagaacguggggguggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7pal Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 4.7 Å
• Binding residue (original residue number in PDB): M1 K2 Y3 I7 F8 K9 R12 R13 K23 K27 G28 R31 G36 Q37 H38 T46 Y50 L54 K57 Q58 T67 D68 K69 Q70 R73 R82 T109 R111 Q115 N118 H119 H121 R127 V129 D130 T131 P132 S133 I134 K147 I151 K201 R202
• Binding residue (residue number reindexed from 1): M1 K2 Y3 I7 F8 K9 R12 R13 K23 K27 G28 R31 G36 Q37 H38 T46 Y50 L54 K57 Q58 T67 D68 K69 Q70 R73 R82 T109 R111 Q115 N118 H119 H121 R127 V129 D130 T131 P132 S133 I134 K147 I151 K201 R202

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pal, PDBe:7pal, PDBj:7pal
• PDBsum: 7pal
• PubMed: 36171285
• UniProt: P46775|RS4_MYCPN Small ribosomal subunit protein uS4 (Gene Name=rpsD)