Structure of PDB 7pas Chain e Binding Site BS01

Receptor Information

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

KIGNRTITLDPAKVNLNFQKDHIAVKGPLGQIELKLPPNLPLKFELKDNN
LQITRNNELKQSKIFHGTYNALITNAIIGVTQGFEKKLRLVGVGYRANVE
GETLNLQLGYSHPIKEKIPKGLTVKVEKNTEITISGISKELVGQFATEVR
KWRKPEPYKGKGVLYFDEVIVRKAGK

Ligand information

>7pas 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: 7pas Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 16.0 Å
• Binding residue (original residue number in PDB): K3 I4 N6 R7 T8 K37 P39 Q54 R57 L61 K62 Q63 K65 I66 F67 G69 T70 Y71 A73 L74 N77 K88 G94 V95 G96 Y97 L110 G111 Y112 S113 H114 K141 E142 G145 Q146 T149 R152 K153 K156 E158 P159 Y160 K161 K163 Y167 D169 K175 K178
• Binding residue (residue number reindexed from 1): K1 I2 N4 R5 T6 K35 P37 Q52 R55 L59 K60 Q61 K63 I64 F65 G67 T68 Y69 A71 L72 N75 K86 G92 V93 G94 Y95 L108 G109 Y110 S111 H112 K139 E140 G143 Q144 T147 R150 K151 K154 E156 P157 Y158 K159 K161 Y165 D167 K173 K176

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