Structure of PDB 5mrc Chain DD Binding Site BS01

Receptor Information

>5mrc Chain DD (length=287) Species: 4932 (Saccharomyces cerevisiae)

PRKANLLKSLARGRVRTSFNKYNLFNLYKKGGVDLKSKSLYQQKWTAKQE
TRAYHGEHLTEKRWQTVFKPKLDSVAQLDIKETPFLLQTFAVLEKRLDFA
LFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSVKPDKVL
EALGAKKPSFQEALKIDKTQIVLWNKYVKEAKTEDPIKLSELEGDEPKAR
KLINLPWQKNYVYGRQDPKKPFFTPWKPRPFLSPFAILPHHLEISFKTCH
AVYLRDPVARPGQSEVISPFDVPVHERAYMYYLRNGK

Ligand information

>5mrc Chain aa (length=1501)

uaagaauaugauguugguucagauuaagcgcuaaauaaggacaugacaca
ugcgaaucauacguuuauuauugagauaauaaauaugugguguaaacgug
aguaauuuuauuaggaauuaaugaacuauagaauaagcuaaauacuuaau
auuauauaaaaaauuuauauaauaaaaaggauauauauauauauauuuau
cuauagucaagccaauaaugguuuagguaguagguuuauuaagaguuaaa
ccuagccaacgauccauaaucgauaaugaaaguuagaacgaucacguuga
cucugaaauauagucaauaucuauaagauacagcagugaggaauauugga
caaugaucgaaagauugauccaguuacuuauuaggaugauauauauauau
auauaaauugauuaaaaauaaaauccauaaauaauuaaaauaaugauauu
aauuaccauauauuuauauggauauauauauauuuuaauaguccugacua
auauuugugccagcagucgcgguaacacaaagagggcgagcguuaaucau
aaugguuuaaaggauccguagaaugaauuauauauaauuuagaguuaaua
aaauuaauuaaagaauuauaauaguaaagaugaaauaauaauaauaauua
uaagacuaauauaugugaaaauauuaauuaaauauuaacugacauugagg
gauuaaaacuagaguagcgaaacggauucgauacccguguaguucuagua
guaaacuaugaauacaauuauuuauaauauauauauaaauaauaaaugaa
aaugaaaguauuccaccugaagaguacguuagcaauaaugaaacucaaaa
caauagacgguuacagacuuaagcaguggagcauguuauuuaauucgaua
auccacgacuaaccuuaccauauuuugaauauuauaauaauuauaauuau
uauauuacaggcguuacauuguugucuuuaguucgugcugcaaaguuuua
gauuaaguucauaaacgaacaaaacuccauauauauaauuuuaauuauau
auaauuuuauauuauuuaauauaaagaaaggaauuaagacaaaucauaau
gauccuuauaauauggguaauagacgugcuauaauaaaaugauaauaaaa
uuauauaaaauauauuuaauuauauuuaauuaauaauauaaaacauuuua
auuuuuaauauauuuuuuuauuauaaauaugaauuauaaucugaaauucg
auuauaugaaaaaagaauugcuaguaauacguaaauuaguauguuacggu
gaauauucuaacuguuucgcacuaaucacucaucacgcguugaaacauau
uauuaucuuauuauuuauauaauauuuuuuaauaaauauuauuaauuuau
auuuauuuauaucagaaauaauaugaauuaaugcgaaguugaaauacagu
uaccguaggggaaccugcggugggcuuauaaauaucuuaaauauucuuac
a

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

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): P2 L7 K9 S10 L11 R13 N21 K22 Y23 L41 Y42 Q43 K45 W46 Q50 E62 K63 R64 S117 R119 Q120 R122 Q123 L126 H127 R131 E159 K164 K165 S167 V180 L181 Y185 P405 W406 P420 R428 M479 R483 N484 G485 K486
• Binding residue (residue number reindexed from 1): P1 L6 K8 S9 L10 R12 N20 K21 Y22 L40 Y41 Q42 K44 W45 Q49 E61 K62 R63 S109 R111 Q112 R114 Q115 L118 H119 R123 E151 K156 K157 S159 V172 L173 Y177 P206 W207 P221 R229 M280 R284 N285 G286 K287

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0032543 mitochondrial translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005763 mitochondrial small ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mrc, PDBe:5mrc, PDBj:5mrc
• PDBsum: 5mrc
• PubMed: 28154081
• UniProt: P27929|NAM9_YEAST Small ribosomal subunit protein uS4m (Gene Name=NAM9)