Structure of PDB 7ood Chain e Binding Site BS01

Receptor Information

>7ood Chain e (length=176) Species: 272634 (Mycoplasmoides pneumoniae M129)

KIGNRTITLDPAKVNLNFQKDHIAVKGPLGQIELKLPPNLPLKFELKDNN
LQITRNNELKQSKIFHGTYNALITNAIIGVTQGFEKKLRLVGVGYRANVE
GETLNLQLGYSHPIKEKIPKGLTVKVEKNTEITISGISKELVGQFATEVR
KWRKPEPYKGKGVLYFDEVIVRKAGK

Ligand information

>7ood Chain 3 (length=2879)

aguuacuaagggcuuaugguggaugccuuggcacuaauaggcgaugaagg
acguguuaaccugcgauaagcuucggguaggugguaagaaccucagaucc
ggagauuuccgaauggagcaauccgguaguuggaaacagcuaucauuaau
ugaugaauaaauagucaauuaaagcaauacguggugaagugaaacaucuc
aguagccacaggaaaagaaaacgaaugugauuccguguguaguggcgagc
gaaagcggaacaggccaaacuuaucauuagauagggguuguagggcuugc
aauguggacuugaaaacgauagaagaagcuguuggaaagcagcgcgcaaa
agggugauagccccguauuugaaauuguuuucauaccuagcgagaucccu
gaguagcucggaaaacguuauuuugagugaaucugcccagaccauugggu
aagccuaaauacuaauuagugaccgauagcgaaacaguaccgugagggaa
aggugaaaagaacccagagaugggagugaaauagauucugaaaccauaug
ccuacaacgugucagagcacauuaaugugugauggcgugcguuuugaagu
augagccggcgaguuaugauagcaagcguuaguuaaccaggagaugggga
gcuguagcgaaagcgaguuuuaaaagagcguuuguuuguuauuauagacc
cgaaacggguugagcuagucaugagcagguugaagguugaguaacaucaa
cuggaggaccgaaccgacucucguugaaacgauagcggaugacuugugau
uaggggugaaauuccaaucgaaauccgugauagcugguucucgucgaaau
agcuuuaaggcuagcgugagaucacaaauaaguggagguaaagcuacuga
auguaugauggcgccaccuaggcguacugaauacaauuaaacucugaaug
ccauuuauuuuauucucgcagucagacagugggggauaagcuucauuguc
aagaggggaagagcccagaucauuaaauaagguccccaaaauauacuaag
uggaaaaggaugugaaagugcuaaaacagcaaggauguuggcuuagaagc
agccaucguuuaaagagugcguaacagcucacuugucgaguguuuuugcg
ccgaagauguaacggggcuaaguauauuaccgaauuuauggauaagauuu
auaucuugugguagacgagcguuguauuggaguugaagucaaagcgugag
cauugguggauccaauacaagugagaaugccggcaugaguaacgcuuggg
agugagaaucucccaaaccgauugacuaagguuuccuggaccagggucgu
ccuuccaggguuagucuggaccuaagcugaggcugaaaagcguaggcgau
ggacaacagguuaauauuccuguacuuacaguuagacugauggagugaca
aagaagguuuuccacccccauaauuggauuuggggauaaaucauaaggug
guacaauaggcaaauccguugugcauaacauugagugaugaugucgagug
aaaguagcgaaggugguauuaaucaugcuuucaagaaaagcuucuagggu
uaaucuagcuguaaccaguaccgagaacgaacacacguagucaaggagag
gauccuaagguuagcgagugaacuauagccaaggaacucugcaaauuaac
cccguaaguuagcgagaaggggugcuuauguaaaaguaagccgcagugaa
gaacgaggggggacuguuuaacuaaaacacaacucuaugccaaaccguaa
ggugauguauauggggugacaccugcccagugcuggaagguuaaagaagg
agguuagcgcaagcgaagcuuuuaacugaagccccagugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuagucggguaaauuccgu
cccgcuugaaugguguaaccaucucuugacugucucggcuauagacucgg
ugaaauccagguacgggugaagacacccguuaggcgcaacgggacggaaa
gaccccgugaagcuuuacuguagcuuaauauugaucaggacauuaucaug
uagagaauagguaggagcaaucgaugcaaguucgcuaggacuuguugaug
cgaaagguggaauacuacccuugguugugugcuguucuaauugguaacug
uuauccaguuucaagacaguguuaggugggcaguuugacuggggcggucg
ccuccuaaaagguaacggaggcguacaaagguaccuucaguacgguugga
aaucguauguagaguguaaugguguaagggugcuugacugugagacauac
aggucgaacaggugagaaaucaggucauagugauccggugguccaguaug
gaauggccaucgcucaacggauaaaagcuacuccggggauaacaggcuga
uacugcccaagaguucauaucgacggcaguguuuggcaccucgaugucga
cucaucucauccucgagcugaagcagguucgaaggguucggcuguucgcc
gauuaaagagauacgugaguuggguucaaaccgucgugagacagguuggu
cccuaucuauugugcccguaggaagauugaagaguguugcuucuaguacg
agaggaccgaagcgaggacaccucuuaugcuccaguuguagcgccagcug
caccgcuggguaguaacgugucuauuagauaaacgcugaaagcaucuaag
ugugaaacuaucucaaagauuaaucuucccauuucgaaaguaagagccgu
caaagacgaugacguugauagguuacagguguaagcauagugauauguug
agcugaguaauacuaauugcucgaggacu

<<<......<<<<.<<<<<<....{[[..[[<<<<<<<[[<<......<<
<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>.....>>>
>>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<
<<<<.........>>>>>>>>>.>>....<<<<<<.....<<....>>..
....>>>>>.>.........<<....>>..<<<<<<.....<<.....>>
....>>>>>>..(((....<<<<<......>>>>>......<<<<<<<<<
.....<....<<<<<<<<<<.<<<...<<<<<......>>>>>((.....
.<<<.....))>>>...>>>...>>>>>>>>>>...>..>>>>>..>>>>
.....<<<<<<<<.......>>>>>>>>......<<<<<..<<<<>>>>>
..)))......]].>>>>>>>.]]...............<<....>>...
.]].........<<<<....>>>>.............}....>>>>>>.>
>>>.......<<<<..<<<<......>>>>..>>>>...<<<........
>>>.<<<<<<....<<<<<<<<<<<<<...<<<...<<<.....>>>...
>>>...<<....>>..<<<<.....>>>>....>>>>>>>>>>>>>..<<
.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>
>>.....>>>...<<<.<<.<<........>>.>>>>>....>>>>>>>>
>...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<
<<<<....>>>>><<<<<<<<....<<<<<<<<<<......<<....<<.
.<<<<<...<.<<<<.....>>>>..>...>>>>>..>>..>>.......
>>>>>>>>>>...>>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>
....<<<......>>>...<<<<.<<<...<<<(((...<<<<<<<....
.......<<..<<<<<<<<<<.......<<<<<.<<...<<<<.......
>>>>...>>.........<<......>>...>>>>>...>>>>>>>>>>.
>>...........))).....>>>>>>>>>>...>>>>>>><<<<<<<..
..>>>>>>>....>>>>>><<<<<<<<<<<<......<<<<<.<<....>
>.>>>>>...>>>>>>>>>>.>>.....>>>>>>.......<<...<<<<
<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....
>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...
>>...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<<...<
<<<...<<<..<<<<<<<<<....(((...>>>>><<..<<<<<..<<<<
<<<<<<<.<<.....>>>>>>>>>....>>>>..>>>>>...>><..<<.
......>>...>>>>>....>>>....>>>>........>>>>>..>>..
...>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<...
..>>>>..>>>>..<<<<<...<<<<<<<<.<<...............<<
<<<.....<..>......>>>>><<<<<<......>>>>>>.........
...<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....
>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<..<<
<<<<..<<....>>...>>>>>>..>>...>>>>>>>>..>>>>><<<<<
<.......>>>>>>........<...........<.<<<.......>>>.
>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>>>>>>>
>...........<<<<<........>>>>>..<<<<<<<..(((.[[...
...<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<.<<<.<<<<..<<<..
.........<<<<<..<<<......<<<<<<<......>>>>>>>...>>
>.............>>>>>..>>>..>>>>.>>>.>>...<<<..<<<<<
.....>>>>>.>>>....>>>>>>>>>..>>>>>..<<<<.....>>>><
<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.....
..>>>>>>.....<<.[.(((>>....>>>>>>>...<<<<..<<<....
..>>>..>>>>.<<<....>>>.>>)))]......<<<<<<<.((..>>>
>..))>>>>>>>.............>>>>..]]>>>>.......<<<<..
.<<<<<<...<<.......>>...>>>>>>....>>>.>.......<<<<
<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>
>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>...
.]]..))).>>>>>>>....<<<<<<<....<<<..<<<<<<<.......
........>>>>>>><<<<<<...<<<<...<<<<<<<<<<<.)))>>>>
>>..>>>>>...>>>>.>>>>>>..<<<....<<<<<...........>>
>>>....>>>.>>>........>>>>>>>...<<..>>.....<<<<<<<
<.........>>>>....<<<<<<<<.<<<....<<<<<....>>>>>..
.>>>..>>>>>.>>>...>>>>....>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ood Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): I4 K62 Q63 K65 I66 T70 A73 N77 G111 Y112 S113 K141 E142 G145 Q146 Y160 K161 K175
• Binding residue (residue number reindexed from 1): I2 K60 Q61 K63 I64 T68 A71 N75 G109 Y110 S111 K139 E140 G143 Q144 Y158 K159 K173

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7ood, PDBe:7ood, PDBj:7ood
• PDBsum: 7ood
• PubMed: 36171285
• UniProt: Q50303|RL6_MYCPN Large ribosomal subunit protein uL6 (Gene Name=rplF)