Structure of PDB 7pib Chain c Binding Site BS01

Receptor Information

>7pib Chain c (length=210) Species: 272634 (Mycoplasmoides pneumoniae M129)

AKLKLIKIDGSFETEPVKLSPGLIAKELKQQPVFDAVLVEQASWRQGTHS
ILTKGEVRGGGKKPYKQKHTGKARQGSTRNPHFVGGGIVFGPKPNRNYSL
KLNKKAHTAALHTVWSEKLASDNTHLVDQNLFNKTEGKTKVMMQFLKSAK
LLDKNVLFVVNTLNTNLEQSTSNIKNVQVKHLDKVSVRDLMLANALLVEK
EVLKALEGKF

Ligand information

>7pib 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: 7pib Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 4.7 Å
• Binding residue (original residue number in PDB): E28 K30 Q32 Q42 T49 H50 S51 I52 L53 T54 K55 G56 V58 R59 G61 K63 Q68 K69 K73 A74 R75 Q76 G77 R80 H83 F84 V85 G86 G87 V90 F91 P93 Y99 L101 K102 N104 K105 K106 A107 H108 K139 T140 K141 Q170 S173 N174 I175 K176 K185 V186
• Binding residue (residue number reindexed from 1): E27 K29 Q31 Q41 T48 H49 S50 I51 L52 T53 K54 G55 V57 R58 G60 K62 Q67 K68 K72 A73 R74 Q75 G76 R79 H82 F83 V84 G85 G86 V89 F90 P92 Y98 L100 K101 N103 K104 K105 A106 H107 K138 T139 K140 Q169 S172 N173 I174 K175 K184 V185

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pib, PDBe:7pib, PDBj:7pib
• PDBsum: 7pib
• PubMed: 36171285
• UniProt: P75579|RL4_MYCPN Large ribosomal subunit protein uL4 (Gene Name=rplD)