Structure of PDB 3j6b Chain L Binding Site BS01

Receptor Information

>3j6b Chain L (length=229) Species: 4932 (Saccharomyces cerevisiae)

TVGIARKLSRDKAHRDALLKNLACQLFQHESIVSTHAKCKEASRVAERII
TWTKRAITTSNSVAQAELKSQIQSQLFLAGDNRKLMKRLFSEIAPRYLER
PGGYTRVLRLEPRANDSAPQSVLELVDSPVMSESHTVNRGNLKMWLLVKS
VINDDANQLPHNPLTLQNLHKVAKFKAEAQLHGEIMLIKQVLLKEMSLPY
DEALENERTQALLKEVYSSSSSYVMVPRP

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

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

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): T2 V3 I5 R7 K8 S10 K13 H15 R16 L19 N22 Q26 H30 I33 S35 T36 H37 A38 K39 R45 E48 R49 T52 W53 R56 N62 E68 S71 Q72 Q74 S75 F78 L79 G81 D82 R84 K85 R101 P102 G103 G104 R107 R110 N116 D117 S118 A119 R140 K144 N163 L165 T166 Q168 N169 K172 K175 F176
• Binding residue (residue number reindexed from 1): T1 V2 I4 R6 K7 S9 K12 H14 R15 L18 N21 Q25 H29 I32 S34 T35 H36 A37 K38 R44 E47 R48 T51 W52 R55 N61 E67 S70 Q71 Q73 S74 F77 L78 G80 D81 R83 K84 R100 P101 G102 G103 R106 R109 N115 D116 S117 A118 R139 K143 N162 L164 T165 Q167 N168 K171 K174 F175

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j6b, PDBe:3j6b, PDBj:3j6b
• PDBsum: 3j6b
• PubMed: 24675956
• UniProt: P22353|RM08_YEAST Large ribosomal subunit protein bL17m (Gene Name=MRPL8)