Structure of PDB 7pas Chain 1 Binding Site BS01

Receptor Information

>7pas Chain 1 (length=59) Species: 272634 (Mycoplasmoides pneumoniae M129)

MKVKSAAKKRFKLTKSGQIKRKHAYTSHLAPHKTTKQKRHLRKQGTVSAS
DFKRIGNLI

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): M1 K2 V3 K4 S5 A6 K8 K9 R10 K12 L13 T14 K15 S16 K20 K22 Y25 T26 S27 H28 L29 A30 P31 K33 T35 K36 Q37 R39 H40 L41 R42 K43 Q44 S50 F52 K53 R54 G56 N57 L58 I59
• Binding residue (residue number reindexed from 1): M1 K2 V3 K4 S5 A6 K8 K9 R10 K12 L13 T14 K15 S16 K20 K22 Y25 T26 S27 H28 L29 A30 P31 K33 T35 K36 Q37 R39 H40 L41 R42 K43 Q44 S50 F52 K53 R54 G56 N57 L58 I59

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:7pas, PDBe:7pas, PDBj:7pas
• PDBsum: 7pas
• PubMed: 36171285
• UniProt: P75447|RL35_MYCPN Large ribosomal subunit protein bL35 (Gene Name=rpmI)