Structure of PDB 7phc Chain c Binding Site BS01

Receptor Information

>7phc Chain c (length=210) Species: 272634 (Mycoplasmoides pneumoniae M129)

AKLKLIKIDGSFETEPVKLSPGLIAKELKQQPVFDAVLVEQASWRQGTHS
ILTKGEVRGGGKKPYKQKHTGKARQGSTRNPHFVGGGIVFGPKPNRNYSL
KLNKKAHTAALHTVWSEKLASDNTHLVDQNLFNKTEGKTKVMMQFLKSAK
LLDKNVLFVVNTLNTNLEQSTSNIKNVQVKHLDKVSVRDLMLANALLVEK
EVLKALEGKF

Ligand information

>7phc 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: 7phc Visualizing translation dynamics at atomic detail inside a bacterial cell.
• Resolution: 9.9 Å
• Binding residue (original residue number in PDB): F35 E41 S44 W45 R46 Q47 T49 T54 K55 G56 R59 G61 K63 Q68 K69 H70 G72 K73 A74 R75 Q76 G77 R80 N81 P82 H83 F84 V85 V90 F91 K94 R97 N98 Y99 K102 N104 K105 K106 H108 G138 K139 T140 K141 M144 Q170 S171 S173 N174 I175 K176 K185 V186 S187 R189
• Binding residue (residue number reindexed from 1): F34 E40 S43 W44 R45 Q46 T48 T53 K54 G55 R58 G60 K62 Q67 K68 H69 G71 K72 A73 R74 Q75 G76 R79 N80 P81 H82 F83 V84 V89 F90 K93 R96 N97 Y98 K101 N103 K104 K105 H107 G137 K138 T139 K140 M143 Q169 S170 S172 N173 I174 K175 K184 V185 S186 R188

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0046677 response to antibiotic

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7phc, PDBe:7phc, PDBj:7phc
• PDBsum: 7phc
• PubMed: 36171285
• UniProt: P75579|RL4_MYCPN Large ribosomal subunit protein uL4 (Gene Name=rplD)