Structure of PDB 7pip Chain h Binding Site BS01

Receptor Information

>7pip Chain h (length=128) Species: 272634 (Mycoplasmoides pneumoniae M129)

IAKINLLGGQAKPGPALASVGINMGEFTKQFNEKTKDKQGEMIPCVITAY
NDKSFDFILKTTPVSILLKQAAKLEKGAKNAKTIVGKITMAKAKEIAQYK
LVDLNANTVEAALKMVLGTAKQMGIEVI

Ligand information

>7pip 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: 7pip Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 9.3 Å
• Binding residue (original residue number in PDB): I9 A10 K11 I12 N13 K68 P71 S73 K84 G85 K87 N88 A89 K90 L112 A114 N115 K122 M123 G126 T127 K129 Q130 M131
• Binding residue (residue number reindexed from 1): I1 A2 K3 I4 N5 K60 P63 S65 K76 G77 K79 N80 A81 K82 L104 A106 N107 K114 M115 G118 T119 K121 Q122 M123

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7pip, PDBe:7pip, PDBj:7pip
• PDBsum: 7pip
• PubMed: 36171285
• UniProt: P75550|RL11_MYCPN Large ribosomal subunit protein uL11 (Gene Name=rplK)