Structure of PDB 7phc Chain i Binding Site BS01

Receptor Information

>7phc Chain i (length=144) Species: 272634 (Mycoplasmoides pneumoniae M129)

KTSMLTKEQANKRRQWYIVDAAGLVLGKLAVKAADLIRGKNKVDFTPNQD
CGDYLIIINSDQVVLTGNKKENEFWYHHSQYIGGIKKVSGRDMLKKQSDK
LVYNAVKGMLPDNRLSRRWITKVHVFKGDKHNMEAQKPTTLNWS

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): T4 S5 M6 L7 K9 Q11 V27 L28 G29 K30 V33 R40 K42 N50 N70 K71 H80 I84 K88 R93 K102 A107 K109 M111 P113 N115 R116 L117 R119 R120 T123
• Binding residue (residue number reindexed from 1): T2 S3 M4 L5 K7 Q9 V25 L26 G27 K28 V31 R38 K40 N48 N68 K69 H78 I82 K86 R91 K100 A105 K107 M109 P111 N113 R114 L115 R117 R118 T121

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7phc, PDBe:7phc, PDBj:7phc
• PDBsum: 7phc
• PubMed: 36171285
• UniProt: P75178|RL13_MYCPN Large ribosomal subunit protein uL13 (Gene Name=rplM)