Structure of PDB 5mrc Chain d Binding Site BS01

Receptor Information

>5mrc Chain d (length=206) Species: 4932 (Saccharomyces cerevisiae)

MKVNHSISRFRPASWFEKTKIIPPQVYIFRNLEYGQVLYSQFPNFSQTQV
DKLFVRPNWSNRKPSLRRDIWKCMCVVNLQNYKQSVHLYQNLCRLRYLRD
VAQRKESDKLRKKDSNGHVWYSGQYRPTYCQEAVADLRESLLKVFENAAK
KPSIYWEDPWRMGDKDKHWNYDVFNALGLEHKLIQRVGNIAREESVILKE
LAKLES

Ligand information

>5mrc 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: 5mrc The structure of the yeast mitochondrial ribosome.
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): K2 V3 N4 H5 S6 R9 F10 R11 W15 K18 T19 K20 L32 N44 K52 R56 P57 W59 R62 R67 R68 D69 R94 Y97 N116 H118 Y121 G123 Q124 R126 R201 K208
• Binding residue (residue number reindexed from 1): K2 V3 N4 H5 S6 R9 F10 R11 W15 K18 T19 K20 L32 N44 K52 R56 P57 W59 R62 R67 R68 D69 R94 Y97 N116 H118 Y121 G123 Q124 R126 R192 K199

Gene Ontology

Molecular Function

• GO:0000150 DNA strand exchange activity
• GO:0003677 DNA binding
• GO:0003697 single-stranded DNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000002 mitochondrial genome maintenance
• GO:0006310 DNA recombination
• GO:0006355 regulation of DNA-templated transcription
• GO:0032543 mitochondrial translation
• GO:0034599 cellular response to oxidative stress
• GO:0090297 positive regulation of mitochondrial DNA replication

Cellular Component

• GO:0005634 nucleus
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mrc, PDBe:5mrc, PDBj:5mrc
• PDBsum: 5mrc
• PubMed: 28154081
• UniProt: Q06630|MHR1_YEAST Large ribosomal subunit protein mL67 (Gene Name=MHR1)