Structure of PDB 7pir Chain b Binding Site BS01

Receptor Information

>7pir Chain b (length=229) Species: 272634 (Mycoplasmoides pneumoniae M129)

MEIRGIFGVKVGMSQVFTTNNERLPITVIYCEPNQVAGVKTEAKDKYSAT
LLSFDTVENKKLNKPQQGFFEKNNLKPTKHLQEIRNMTGFEMGQQITPQN
LFQVGEYVDVSAISKGRGFTGAIKRWNFKIGPLGHGAGYPHRFQGSVQAG
RGGASAQRVFKGKKMSGHYGHEKVTVQNLRIVGFDEANMLVLVSGAIAGP
EGGVVLIRTAKKKPGVVKPIELAVQTEKA

Ligand information

>7pir 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: 7pir Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 12.1 Å
• Binding residue (original residue number in PDB): I3 M13 S14 Q15 R23 D45 K46 Y47 K60 K61 N63 K64 P65 F69 K72 Q82 E83 K115 G116 R117 G118 F119 T120 G121 K124 R125 F128 K129 I130 L133 G134 H135 G136 A137 G138 Y139 P140 H141 R142 F143 Q144 G145 S146 V147 Q148 A149 G150 R151 G152 G153 A154 S155 A156 Q157 R158 V159 K163 M165 S166 H168 H171 K173 V174 Q177 N178 R180 A196 I197 A198 G199 R208 K211 K212
• Binding residue (residue number reindexed from 1): I3 M13 S14 Q15 R23 D45 K46 Y47 K60 K61 N63 K64 P65 F69 K72 Q82 E83 K115 G116 R117 G118 F119 T120 G121 K124 R125 F128 K129 I130 L133 G134 H135 G136 A137 G138 Y139 P140 H141 R142 F143 Q144 G145 S146 V147 Q148 A149 G150 R151 G152 G153 A154 S155 A156 Q157 R158 V159 K163 M165 S166 H168 H171 K173 V174 Q177 N178 R180 A196 I197 A198 G199 R208 K211 K212

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:7pir, PDBe:7pir, PDBj:7pir
• PDBsum: 7pir
• PubMed: 36171285
• UniProt: P75580|RL3_MYCPN Large ribosomal subunit protein uL3 (Gene Name=rplC)