Structure of PDB 5mrf Chain E Binding Site BS01

Receptor Information

>5mrf Chain E (length=274) Species: 4932 (Saccharomyces cerevisiae)

PKSACSLVKPVHHLVKIDKSKLSPRFPELKYDKSDIRSPGFKPKDTHADR
LNDHYLNTLQSDLLLINYSHNAAVVKGLKQRAWSGDSPYHLNRPPKNPRG
SKAQLPDIHPIKWSNIPGLESVVINCFVREARENQLLAITAALQLQQITG
CKPHPIFSKNDVPTWKLRKGHQMGAKVELKGKEMSQFLSTLTEIVLPRIR
EYKGISNQSGNRFGGISFGLTAEDIKFFPEIDANQDSWPKTFGMHININT
SAQLDYQARTLLSGFQFPFFGEEK

Ligand information

>5mrf Chain A (length=2709)

guagaauaauagauuugaaauauuuauuauauagauuuaaagagauaauc
auggaguauaauaauuaaauuuaauuuaauauaacuauuaauagaagguu
acuaauaaauuaauaauuaauuuuaaaaccuaaagguaaaccuuuauauu
aauaauguuaugaauaauuauuaauaauaauaaacuaagugaacugaaac
aucuaaguaacuuaaggauaagaaaucaacagagauauuaugaguauugg
ugagagaaaauaauaaaggucuaauaaguauuaugugaaaaaaauguaag
aaaauaggauaacaaauucuaagacuaaauacuauuaauaaguauaguaa
guaccguaagggaaaguaugaaaaugauuauuuuauaagcaaucaugaau
auauuauauuauauuaaugauguaccuuuuguauaaugggucagcaagua
auuaauauuaguaaaacaauaaguuauaaauaaauagaauaauauauaua
uauaaaaaaauauauauuuaauuaauauuaauugacccgaaagcaaacga
ucuaacuaugauaagauggauaaacgaucgaacagguugauguugcaaua
ucaucugauuaauugugguuaguagugaaagacaaaucugguuugcagau
agcugguuuucuaugaaauauauguaaguauagccuuuauaaauaauaau
uauuauauaauauauuauauaaagaaugguacagcaauuaauauauauua
gggaacuaguuuuuuaauaauauuaaaucucgaaauauuuaauuauauau
aauaaagagucagauuaugugcgauaagguaaauaaucuaaagggaaaca
gcccagauuaagauauaaaguuccuaauaaauaauaagugaaauaaauau
uaaaauaaauauuuaaaaucaaauauauauauauuuguuaauagauaaua
uacggaucuuaauaauaagaauuauuuaauuccuuggaauauuauauuuu
aaaauauaaauacugaauaucuaaauauuauuauuauaauaauaauaaua
ugguaauagaacauuuaaugauaauauauauuaguuauuaauuaauauau
guauuaauuaaauagagaaugcugacaugaguaacgaaaaaaagguauaa
accuuuucaccuaaaacauaagguuuaacuauaaaaguacggccccuaau
uaaauuaaauauaaauauauuuaagaugggauaaucuauauuaauauuua
ucuuaaaauauauaauuauauuauauauuauauauuuauauaauauaaac
uaauaaagaucaggaaaauuaauguauaccguaauguagaccgacucagg
uauguaaguagagaauaugaaggugaauuagauaauuaaagggaaggaac
ucggcaaagauagcucauaaguuagucaauaaagaguaauaagaacaaag
uuguacaacuguuuacuaaaaacaccgcacuuugcagaaacgauaaguuu
aaguauaaggugugaacucugcuccaugcuuaauauauaaauaaaauuau
uuaacgauaauuuaauuaaauuuagguaaauagcagccuuauuaugaggg
uuauaauguagcgaaauuccuuggccuauaauugaggucccgcaugaaug
acguaaugauacaacaacugucuccccuuuaagcuaagugaaauugaaau
cguagugaagaugcuauguaccuucagcaagacggaaagacccuaugcag
cuuuacuguaauuagauagaucgaauuauuguuuauuauauauaaugaua
auucuaaucuuauacuuaauucuuaaguaauauauaauauauauauauau
uauauauuauaagagacaaucucuaauugguaguuuugauggucauuauc
agcaaaaguaucugaauaaguccauaaauaaauauauaaaauuauugaaa
aaaauaauauauauuauauauauuaauuauaaauugaaauauguuuaauu
gaauauauuuuaguaauagauaaaaauauguacaguaaaauuguaaggaa
aacaauaauaacuuucucggaaagaauuaaauuaauauaaugguauaacu
gugcgauaauuguaacacaaacgagugaaacaaguacguaaguauggcau
aaugaacaaauaacacugauuguaaagguuauugauaacgaauaaaaguu
acgcuagggaaggguaauauagcgaaagaguagauauuguaagcuauguu
ugccaccuucgacucaacauuuccucuugguuguaaaagcuaagaagggu
uugacuguucgucaauuaaaauguuacgugaguuggguuaaauacgaugu
gaaucaguaugguuccuaucugcugaaggaaauauuaucaaauuaaaucu
cauuauuaguacgcaaggaccauaaugaaucaacccaugguguaucuauu
gauaauaauauaauauauuuauuaauauauuaucuauauuaguuuauauu
uuaauuauuaucauaguagauaagcuaaguugauaauaaauaaauauuga
auacauauuaaauaugaaguuguuuuaauaagauaauuaaucugauaauu
uuauacuaaaauuaauaauuauagguuuuauauauuauuuauaauuauaa
uauuaauaaaauacuaauuuaucaguuaucuauauaauaucuaaucuauu
auucuauau

<<<<<<<<<<<<<<<.<<......<<<<<<<<<<<<.....<<<<<<<<<
<<...<<<<....<<<<<<<<.>>>>>>>>...<<<<<<<<<<..<<<<.
......<<<<<<<...>>>>>>>....>>>>..<<<....>>>....<<<
<<<<<<..<....>..>>>>>>>>>.........<<<<<<.....<<...
.>>......>>>>>.>..<<.....<<....>>..<<<<<<.....<<..
...>>....>>>>>>...<<<.........<<<<<<.......>>>>>>.
.....<<<<..((((.>>>>..>>>....>>.>>>>>>>>.>>.......
...<<....>>....>>>>....>>>>>>>>>>>.......<<<<<.<<<
<<<......>>>>>>.>>>>>...<.<........>.>.<<<<<<....<
<<<<<<<<<<<<..<<<.....>>>....................<<<<.
<......>.>>>>.......>>>>>>>>>>>>>..<<.<..<<<<<<<..
..<<<<<<<<<<..<<<<......>.>>>...<<<..<<<<........>
>>>.>>>....>>>>>>>>>>...<<.....>>.......>>>>>>...>
..>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<..<..<<<<<
<<<<<<<<<<<..>>>>>>>>>..<<<<...<<<...<<<<<<<.<<<<<
<<<<<<<>>>>>>>>>>>>>>>>>>>..>>.>...>>>>>>>>>>>...>
.>>>>>>.>>..<<<<<<.<<<......>>>.>>>>>>....<<<.....
.>>>...<<<.<<<<...<<<(((...<<<<<<<.....<<......<<<
<<<<<<<..>>>>>.....<<<<<<<<..>>>>>>>>.>>>>>.......
...)))>>.............>>>>>>><<<<<..>>>>>.<<<<<<<<.
.>>>>>>>>..>>>...>>>>>>><<<<<<<<<<<<...>>>>>>>>>>>
>....>>>>>>..<<<<<<......<<<<<<<<<<<...>>>>>>>>>>>
......>>>>>>........>>>>>><......<<....<<<<<<.....
.>>>>>><<<<<...<<<<<.<.............((..<<<.<<<...<
<<...<..<<<<..>>>>>..>>>...>>>.....)).<<<<<<<.<<<.
....<<.<<<......>>>.>>.<<<<<<<<<<<..>>>>>>>>>.[[..
>>....>>>........>>>>>>>....>>>...>.....<<......>>
>>>>>..<<<.....>>>..>>>>>..<<<<....<<<<<<<<.<<....
.............<<<....<.....>......>>>.............<
<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>>
......>>>>>>>..<<<<.<<<..<<<<<<<<.<<.....<.<<<<<<<
<....>>>>>>>>>.....>>>>>>>>..>>>>><<<<<........>>>
>>........<...........<<<<<.......>>>>>.....>....>
>.>>..>>.>>>>>>......>>.>>>>>>>>.>>>>>>.....>.....
<<<<<........>>>>>..<<<<<<<<.<<<.<<<....<<<<<.<<<<
<<..<<<<.<<<<<<<..<<<.<<<<<<<<<<<.<<.....>>>>>>>>>
>>>>...<<<<<<<<<.<....>.>.>>.<<<<<<<<<<<<<..>>>>>>
>>>>>>>.>>>>>>....>>>>>>>>>>..>>>>..<<<<.>>>><<<<<
<...........>>>.>>>..<<....<<<.....<<<....>>>.....
.....<<<<<<<.....>>>>>>>...>>>.....<<<<<<<<<<<....
>>>>>>>>>>>.................<<<<<<<....<<<<<......
.>>>>><<<..<<<<<<.>>>>>>.>>>......<<.[.(((>>....>>
>>>>>....<<<<..<<<......>>>..>>>>.<<<....>>>.>>)))
].......<<<<<<.<<..))))..>>>>>>>>.............>>>>
..>>>>>>>..<<<<.<.<<<<<....<<.......>>....>>>>>...
>>>>.>..<<<<<..<<<<<..<<<<<<<<<.......>>>>>>>..>>.
<<<<<.....>>>>>.....>>>>>......>>>.>>....<<<<<<<..
..>>>.>>>>...>>>..>>>>>>>>>>>.....<<<<<..<<<<<<..<
<<<<<<...............>>>>>>><<<<<<....<<<..<<<<<<<
<<<<<<<<.<<<<<<<<<<....>>>>>>>>>>..<<<<...]].>>>>.
....>>>>>>>>>..>>>>>>..>>>..>>>>>>..<<<.<..<<<<<..
..........>>>>>...>>>>.>>>>>>..>>>>>.....<<<<<<<<<
<.......>>>>>........<<<<<<<<<<..<<...<<<<<..>>>>>
.>>..>>>>>>>.>>>....>>>>>..>>>>>>>>>>>>>>.>>>>>>>>
>>>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mrf The structure of the yeast mitochondrial ribosome.
• Resolution: 4.97 Å
• Binding residue (original residue number in PDB): P19 K20 A22 S24 V26 K34 K37 L40 S41 P42 R43 F44 L47 K51 K97 Q98 R99 W101 P106 Y107 N110 R111 R117 A121 Q122 L123 P124 D125 W131 S132 N143 F145 R147 Q153 K170 I174 F175 S176 K177 N178 W183 L185 K187 G188 K194 S227 G228 N229 R230 F231 S235 F236 G237 G261 M262 H263 N265 N267 K292
• Binding residue (residue number reindexed from 1): P1 K2 A4 S6 V8 K16 K19 L22 S23 P24 R25 F26 L29 K33 K79 Q80 R81 W83 P88 Y89 N92 R93 R99 A103 Q104 L105 P106 D107 W113 S114 N125 F127 R129 Q135 K152 I156 F157 S158 K159 N160 W165 L167 K169 G170 K176 S209 G210 N211 R212 F213 S217 F218 G219 G243 M244 H245 N247 N249 K274

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mrf, PDBe:5mrf, PDBj:5mrf
• PDBsum: 5mrf
• PubMed: 28154081
• UniProt: P36519|RM07_YEAST Large ribosomal subunit protein uL5m (Gene Name=MRPL7)