Structure of PDB 7ph9 Chain m Binding Site BS01

Receptor Information

>7ph9 Chain m (length=119) Species: 272634 (Mycoplasmoides pneumoniae M129)

SYINKPGKTSAWRVMTVRQQVSAVLAYGKIETTLKKAKNTQKRLDKLITL
AKVDNFNNRRQVKKWLLNTNLFDVDQLMDHLFSKVAPKYEKTPGGYSRVL
KLGPRRGDATEMAILQLTD

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): S2 Y3 I4 K6 P7 K9 T10 S11 W13 R14 V15 M16 Q20 Q21 Y28 K30 I31 E32 K36 K37 K43 D46 K47 T50 F57 R60 R61 K64 K65 L68 N69 T70 N71 P94 G95 G96 S98 R99 R106 R107 G108 D109 T111
• Binding residue (residue number reindexed from 1): S1 Y2 I3 K5 P6 K8 T9 S10 W12 R13 V14 M15 Q19 Q20 Y27 K29 I30 E31 K35 K36 K42 D45 K46 T49 F56 R59 R60 K63 K64 L67 N68 T69 N70 P93 G94 G95 S97 R98 R105 R106 G107 D108 T110

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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: Q59547|RL17_MYCPN Large ribosomal subunit protein bL17 (Gene Name=rplQ)