Structure of PDB 7pas Chain i Binding Site BS01

Receptor Information

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

KTSMLTKEQANKRRQWYIVDAAGLVLGKLAVKAADLIRGKNKVDFTPNQD
CGDYLIIINSDQVVLTGNKKENEFWYHHSQYIGGIKKVSGRDMLKKQSDK
LVYNAVKGMLPDNRLSRRWITKVHVFKGDKHNMEAQKPTTLNWS

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 T4 S5 L7 Q11 A12 K14 V27 L28 G29 K30 V33 D37 R40 K42 P49 N50 Q51 T68 G69 N70 K71 N74 E75 Y78 H79 H80 S81 Q82 Y83 I84 G85 G86 K89 R93 D94 K98 Q99 D101 K102 Y105 A107 K109 G110 M111 L112 D114 N115 R116 L117 R119 R120 W121 T123 H126 N134 M135 Q138
• Binding residue (residue number reindexed from 1): K1 T2 S3 L5 Q9 A10 K12 V25 L26 G27 K28 V31 D35 R38 K40 P47 N48 Q49 T66 G67 N68 K69 N72 E73 Y76 H77 H78 S79 Q80 Y81 I82 G83 G84 K87 R91 D92 K96 Q97 D99 K100 Y103 A105 K107 G108 M109 L110 D112 N113 R114 L115 R117 R118 W119 T121 H124 N132 M133 Q136

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