Structure of PDB 3j6b Chain P Binding Site BS01

Receptor Information

>3j6b Chain P (length=207) Species: 4932 (Saccharomyces cerevisiae)

DINVSEKIYKWTKAGIEQGKEHFKVGGNKVYFPKARIILLRPNAKHTPYQ
AKFIVPKSFNKLDLRDYLYHIYGLRAMNITTQLLHGKFNRMNLQTTRFRE
PQIKKMTIEMEEPFIWPEEPRPDENSFWDSTTPDNMEKYREERLNCLGSD
ANKPGTAFDGVVGPYERVAQPFIPRFLKREIDNKRERHAAELQRADKLIA
LNRYIED

Ligand information

>3j6b Chain A (length=2713)

guagaauaauagauuugaaauauuuauuauauagauuuaaagagauaauc
auggaguauaauaauuaaauuuaaauuuaauauaacuauuaauagaaggu
uacuaauaaauuaauaauuaauuuuaaaaccuaaagguaaaccuuuauau
uaauaauguuaugaauaauuauuaauaauaauaaacuaagugaacugaaa
caucuaaguaacuuaaggauaagaaaucaacagagauauuaugaguauug
gugagagaaaauaauaaaggucuaauaaguauuaugugaaaaaaauguaa
gaaaauaggauaacaaauucuaagacuaaauacuauuaauaaguauagua
aguaccguaagggaaaguaugaaaaugauuauuuuauaagcaaucaugaa
uauauuauauuauauuaaugauguaccuuuuguauaaugggucagcaagu
aauuaauauuaguaaaacaauaaguuauaaauaaauagaauauauauaaa
aaaauauauuaaauauuuaauuaauauuaauugacccgaaagcaaacgau
cuaacuaugauaagauggauaaacgaucgaacagguugauguugcaauau
caucugauuaauugugguuaguagugaaagacaaaucugguuugcagaua
gcugguuuucuaugaaauauauguaaguauagccuuuauaaauaauaauu
auuauauaauauauuauauaaagaaugguacagcaauuaauauauauuag
ggaacuaguuuuuuaauaauauuaaaucucgaaauauuuaauuauauaua
auaaagagucagauuaugugcgauaagguaaauaaucuaaagggaaacag
cccagauuaagauauaaaguuccuaauaaauaauaagugaaauaaauauu
aaaauauuaauauuuaaaaucaaauauauauauauuuguuaauagauaau
auacggaucuuaauaauaagaauuauuuaauuccuuggaauauuauauuu
uaaaauauaaauacugaauaucuaaauauuauuauuacuaauaauaauaa
uaugguaauagaacauuuaaugauaauauauauuaguuauuaauuaauau
auguauuaauuaaauagagaaugcugacaugaguaacgaaaaaaagguau
aaaccuuuucaccuaaaacauaagguuuaacuauaaaaguacggccccua
auuaaauuaaauauaaauauauuuaagaugggauaaucuauauuaauaau
uuaucuuaaaauauauaauuauauuauauauuauauauuuauauaauaua
aacuaauaaagaucaggaaaauuaauguauaccguaauguagaccgacuc
agguauguaaguagagaauaugaaggugaauuagauaauuaaagggaagg
aacucggcaaagauagcucauaaguuagucaauaaagaguaauaagaaca
aaguuguacaacuguuuacuaaaaacaccgcacuuugcagaaacgauaag
uuuaaguauaaggugugaacucugcuccaugcuuaauauauaaauaaaau
uauuuaacgauaauuuaauuaaauuuagguaaauagcagccuuauuauga
ggguuauaauguagcgaaauuccuuggccuauaauugaggucccgcauga
augacguaaugauacaacaacugucuccccuuuaagcuaagugaaauuga
aaucguagugaagaugcuauguaccuucagcaagacggaaagacccuaug
cagcuuuacuguaauuagauagaucgaauuauuguuuauuauauauaaug
auaauucuaaucuuauacuuaauucuuaaguaauauauaauauauauaua
uauuauauauuauaagagacaaucucuaauugguaguuuugauggucauu
aucagcaaaaguaucugaauaaguccauaaauaaauauauaaaauuauug
aaaaaaauaauauauauuauauauauuaauuauaaauugaaauauguuua
auugaauauauuuuaguaauagauaaaaauauguacaguaaaauuguaag
gaaaacaauaauaacuuucucggaaagaauuaaauuaauauaaugguaua
acugugcgauaauuguaacacaaacgagugaaacaaguacguaaguaugg
cauaaugaacaaauaacacugauuguaaagguuauugauaacgaauaaaa
guuacgcuagggaaggguaauauagcgaaagaguagauauuguaagcuau
guuugccaccuucgacucaacauuuccucuugguuguaaaagcuaagaag
gguuugacuguucgucaauuaaaauguuacgugaguuggguuaaauacga
ugugaaucaguaugguuccuaucugcugaaggaaauauuaucaaauuaaa
ucucauuauuaguacgcaaggaccauaaugaaucaacccaugguguaucu
auugauaauaauauaauauauuuaauauauuaucuauauuaguuuauauu
uuaauuauauauuaucauaguagauaagcuaaguugauaauaaauaaaua
uugaauacauauuaaauaugaaguuguuuuaauaagauaauuaaucugau
aauuuuauacuaaaauuaauaauuauagguuuuauauauuauuuauaauu
auaauauuauaaaaauacuaauuuaucaguuaucuauauaauaucuaauc
uauuauucuauau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j6b Structure of the yeast mitochondrial large ribosomal subunit.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): N57 V58 I62 W65 F77 K78 N82 K83 K88 A89 L94 R95 N97 K99 K106 P110 K111 S112 N114 K115 R119 T134 T135 Q136 L137 L138 H139 K141 F142 R144 Q148 T150 R151 K158 K159 T161 R229 F230 R233 E234 N237
• Binding residue (residue number reindexed from 1): N3 V4 I8 W11 F23 K24 N28 K29 K34 A35 L40 R41 N43 K45 K52 P56 K57 S58 N60 K61 R65 T80 T81 Q82 L83 L84 H85 K87 F88 R90 Q94 T96 R97 K104 K105 T107 R175 F176 R179 E180 N183

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j6b, PDBe:3j6b, PDBj:3j6b
• PDBsum: 3j6b
• PubMed: 24675956
• UniProt: P32387|RM41_YEAST Large ribosomal subunit protein uL23m (Gene Name=MRP20)