Structure of PDB 3j6b Chain J Binding Site BS01

Receptor Information

>3j6b Chain J (length=220) Species: 4932 (Saccharomyces cerevisiae)

VSILGQLKPSDGSTKSFKRLGRGPSSGLGKTSGRGQKGQKARGKVKSWFE
GGQTPIYKLFPKIGFTNVGAKPLKELNLKRIQWFHDKNRLHLQPGEVLDM
NKMRKLGLVTGPIKYGVKILASGKFHYNLPIALEASRASAKAIAAIEKAG
GKFTARYYTPLGLRAHLNPQWFLEKRGRVPLQARPTKRRDIDFYSKEEKR
GYLVMEKDKLLQDIKEAQNK

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): L61 G62 L64 K65 S67 D68 G69 T71 K72 F74 K75 R76 G78 R79 G80 S82 S83 G86 K87 T88 S89 G90 R91 G92 Q93 K94 G95 Q96 K97 R99 K103 S104 W105 F106 E107 G108 G109 Q110 T111 K115 L116 F117 P118 K119 I120 G121 F122 N124 V125 E132 N134 R137 W140 R146 T167 P169 K175 L177 A178 K181 R194 S196 K198 L218 R221 W228 R235 L238 A240 R241 T243 K244 R245 R246 D249 F250 K253 K256
• Binding residue (residue number reindexed from 1): L4 G5 L7 K8 S10 D11 G12 T14 K15 F17 K18 R19 G21 R22 G23 S25 S26 G29 K30 T31 S32 G33 R34 G35 Q36 K37 G38 Q39 K40 R42 K46 S47 W48 F49 E50 G51 G52 Q53 T54 K58 L59 F60 P61 K62 I63 G64 F65 N67 V68 E75 N77 R80 W83 R89 T110 P112 K118 L120 A121 K124 R137 S139 K141 L161 R164 W171 R178 L181 A183 R184 T186 K187 R188 R189 D192 F193 K196 K199

Gene Ontology

Molecular Function

• 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:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j6b, PDBe:3j6b, PDBj:3j6b
• PDBsum: 3j6b
• PubMed: 24675956
• UniProt: P36520|RM10_YEAST Large ribosomal subunit protein uL15m (Gene Name=MRPL10)