Structure of PDB 7pir Chain v Binding Site BS01

Receptor Information
>7pir Chain v (length=63) Species: 272634 (Mycoplasmoides pneumoniae M129) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKKDQLTLRGPLYGNNRSHSKTITRRKWNVNLQPCKVKTADGKTTRILVS
TRTLRTLKKHNRL
Ligand information
>7pir Chain 3 (length=2878) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

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PDB7pir Visualizing translation dynamics at atomic detail inside a bacterial cell.
Resolution12.1 Å
Binding residue
(original residue number in PDB)
A2 K3 R10 L13 Y14 R18 S19 H20 S21 K22 T23 I24 R26 W29 N30 V31 N32 Q34 P35 C36 K37 D42 K44 T45 R47 T52 R53 R56 T57 K59 K60 H61
Binding residue
(residue number reindexed from 1)
A1 K2 R9 L12 Y13 R17 S18 H19 S20 K21 T22 I23 R25 W28 N29 V30 N31 Q33 P34 C35 K36 D41 K43 T44 R46 T51 R52 R55 T56 K58 K59 H60
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:7pir, PDBe:7pir, PDBj:7pir
PDBsum7pir
PubMed36171285
UniProtP75171|RL28_MYCPN Large ribosomal subunit protein bL28 (Gene Name=rpmB)

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