Structure of PDB 7ph9 Chain l Binding Site BS01

Receptor Information

>7ph9 Chain l (length=136) Species: 272634 (Mycoplasmoides pneumoniae M129)

MLQPKRTKYRKPHNVSYEGKAKGNSYVAFGEYGLVATKGNWIDARAIESA
RIAISKCLGKTGKMWIRIFPHMSKTKKPLEVRMGSGKGNPEFWVAVVKQG
TVMFEVANIPESQMIKALTRAGHKLPVTWKILKREE

Ligand information

>7ph9 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: 7ph9 Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 8.7 Å
• Binding residue (original residue number in PDB): P4 K5 R6 K8 Y9 R10 K11 P12 H13 N14 V15 E18 K22 G23 N24 Y26 F29 W41 R45 A46 E48 S49 K56 W65 R67 F69 K74 K76 K77 L79 E80 V81 R82 M83 G84 S85 G86 K87 R120 H123 K124 L125 P126
• Binding residue (residue number reindexed from 1): P4 K5 R6 K8 Y9 R10 K11 P12 H13 N14 V15 E18 K22 G23 N24 Y26 F29 W41 R45 A46 E48 S49 K56 W65 R67 F69 K74 K76 K77 L79 E80 V81 R82 M83 G84 S85 G86 K87 R120 H123 K124 L125 P126

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:7ph9, PDBe:7ph9, PDBj:7ph9
• PDBsum: 7ph9
• PubMed: 36171285
• UniProt: P41204|RL16_MYCPN Large ribosomal subunit protein uL16 (Gene Name=rplP)