Structure of PDB 3j6b Chain R Binding Site BS01

Receptor Information

>3j6b Chain R (length=318) Species: 4932 (Saccharomyces cerevisiae)

SRTSMKDSAGRRLGPKKYEGQDVSTGEIIMRQRGTKFYPGENVGIGKDHS
IFALEPGVVRYYLDPFHPKRKFIGVALRRDLKLPSPHFEPTVRRFGRFEL
TNKRAAYKEENSISRKDYLAKPNILKQLEVRESKRKELQDKLSKVLRDEL
KLDDIELATSYLIRVRASLKNGYPIEDARFNSRYYLKEEERLKARRESWT
NEKLSESLSKIDECSDLLNSSTSFNNKLELHQYISEQEKQALKAKLLEDL
EKSQHLETKKDKNYIKALFKDACNFLTLSEEVHLRRKYLKSVFPVSRRFD
YTKVEVIARSRRAFLSKL

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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....)))>>.............>>>>>>><<<<<..>>>>>.<<<<<<<<
..>>>>>>>>..>>>...>>>>>>><<<<<<<<<<<<....>>>>>>>>>
>>>....>>>>>>..<<<<<<......<<<<<<<<<<<...>>>>>>>>>
>>......>>>>>>........>>>>>><......<<....<<<<<<...
...>>>>>><<<<<...<<<<<.<.............((..<<<.<<<..
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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): T37 S38 M39 K40 D41 S42 G44 R45 R46 L47 K50 Y52 E53 G54 Q55 T59 G60 E61 I62 R65 R67 G68 T69 K70 F71 Y72 G80 K81 D82 H83 F86 Y95 H101 K103 R104 R113 F132 N136 R138 A139 K142 S148 R149 K150 Y152 L162 R165 R169 K206 N207 G208 K263 S315 E317 V318 H319 L320 R321 R322 K323 S327 V328 P330 S347 R348 R349 V357 L371
• Binding residue (residue number reindexed from 1): T3 S4 M5 K6 D7 S8 G10 R11 R12 L13 K16 Y18 E19 G20 Q21 T25 G26 E27 I28 R31 R33 G34 T35 K36 F37 Y38 G46 K47 D48 H49 F52 Y61 H67 K69 R70 R79 F98 N102 R104 A105 K108 S114 R115 K116 Y118 L128 R131 R135 K170 N171 G172 K227 S279 E281 V282 H283 L284 R285 R286 K287 S291 V292 P294 S296 R297 R298 V304 L318

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation
• GO:0033617 mitochondrial cytochrome c oxidase assembly

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: P12687|RM02_YEAST Large ribosomal subunit protein bL27m (Gene Name=MRP7)