Structure of PDB 6n8j Chain e Binding Site BS01

Receptor Information

>6n8j Chain e (length=127) Species: 559292 (Saccharomyces cerevisiae S288C)

ASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNIS
QPKIGYGSNKKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNIS
AKNRVVILARAKALGIKVTNPKGRLAL

Ligand information

>6n8j Chain 1 (length=3047)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaauc
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuagacagccggacgguggccauggaagucg
gaauccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccu
gaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguug
auaugaugcccugacgaguaggcaggcguggaggucagugacgaagccua
gaccguaaggucgggucgaacggccucuagugcagaucuuggugguagua
gcaaauauucaaaugagaacuuugaagacugaaguggggaaagguuccac
gucaacagcaguuggacguggguuagucgauccuaagagauggggaagcu
ccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgg
uuaagauuccggaaccuggauauggauucuucacgguaacguaacugaau
guggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaaca
gcuuaucaccccggaauugguuuauccggagauggggucuuauggcugga
agaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaa
auccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagc
aggucuccaaggugaacagccucuaguugauagaauaauguagauaaggg
aagucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggg
ucggguacgaucaacuuagaacugguacggacaaggggaaucugacuguc
uaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugu
gauuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcg
cggguaaacggcaauggauuaacgagauucccacugucccuaucuacuau
cuagcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaa
gaagacccuguugagcuugacucuaguuugacauugugaagagacauaga
ggguaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauuc
auuuuccacguucuagcauucaaggucccauucggggcugauccggguug
aagacauugucagguggggaguuuggacaucuguuaaacgauaacgcaga
uguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagg
guaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaag
uguggccuaucgauccuuuagucccucggaauuugaggcuagaggugcca
gaaaaguuaccacagggauaacuggcuuguggcagucaagcguucauagc
gacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagc
agaauucgguaagcguuggauuguucacccacuaauagggaacgugagcu
ggguuuagaccgucgugagacagguuaguuuuacccuacugaugaauguu
accgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaa
uugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgc
uggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggug
auuucuuugcuccacacaauauagauggauacgaauaaggcguccuugug
gcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggcc
uugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauca
uuuguauacgacuuagauguacaacgggguauuguaagcaguagaguagc
cuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[...........<<.<<<<<<...>>>>>>.>>........
.....<<<<<<.<<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<<<..>>>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<...<<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<......>...>>>.>>>.>>....>>>>>>.>>>>>>>.<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<<.<<.<<........>>>>>>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<......
>>>.....>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>
>>>.>>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<.
.....>>>...<<<<<<<..<<<<(((.....<<<<<<......<.....
.....<<<.<<<<<<<<<<.......<<<<<.<<....<<.........>
>....>>.........<<......>>...>>>>>...>>>>>>>>>>>>>
..........))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<..
.......>>>>>>>>>....>>>>>><<<<<<<<<..<<......<<<<.
<<<<....>>>>>>>>...>>.>>>>>>>.>>.....>>>>>><<.....
<<.....<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<
<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<....>
>>........<<<<<<........>>>>>>....>>....>>...<<<<<
........>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<
<<<<<...<<<<.<<<<<<<<<<<<<<<<<<..{{{..>>>>>>....<<
<<<....<<<<<<....<<<.....>>>....>>>>>>.....>>>>>..
...<<<<<<<<....>>>>>>>>>>>>.>.>>>>>>>.>>>>........
.>>>>>>..........>>>..>>>>>>>>>>>>..>>.....<<.....
.>>>>>>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.
........<.....<<<<<.....<..>......>>>>><<.<<<<<<<<
<<<....>>>>>..>>>>>>.>>............<<<<<<<<<..<<<.
........>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>
...<<...<<..<<<<<<.<..<<<....<<<<<....>>>>.>...>>>
>>>>>..>>>>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>
>>>>>....>>....<<<<<........>>>>>....[[[[[..{{{...
.....[[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<<<.<<<.
<.....>.>>>..>>>>>>>>>>...<<<<<.....<<<<..<<<<<...
...>>>>>...............<<<<<<....>>>>>>..>>>>..>>>
>>.....>>>>>>>>..>>>>>......<<<<<<...........>>>>>
>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(((
>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>
>>.>>))).......((((((..((((.>>>>>>))))))))))......
....]]]]..}}]]]]]..............<<<<<...<<.......>>
...>>>>>...................<<<.<.<<<<..<.<<<<<<<..
....>>>>>>>...>.<<<.........>>>.....>>>>...>...>>>
.......<<<<<<<....>>>.>>>>........}}}.]]]]]....<<<
<<<<<..<<<<.<.<<<<<<...............>>>>>>.><<<<<..
.<<<<....<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>..>>>>>.
<<<<...<<<<<...........>>>>>...>>>>.>>>>....>>>>>>
>>.......<<<<<<.<<<.<.....<<...........<<<<<.....>
>>>>.......>>.......<<<<<<...<<<<<.<..<<<......>>>
..>.>>>>>.>>>>>>..............>.>>>.>>>>>>..<<<<<.
<.............>.....<<<<<<<<<.<<<....<<<<....<<.<.
........>>>...>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6n8j Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): K11 K12 K15 F17 R19 H21 D23 R24 Y25 H26 R27 N31 W32 R33 K34 K36 G37 I38 D39 R43 R45 F46 R47 P53 K54 I55 G56 G58 S59 N60 K61 F65 P68 N78 E95 A97 H98 N99 S101 A102 N104 R105 K118 N121 G124 R125
• Binding residue (residue number reindexed from 1): K10 K11 K14 F16 R18 H20 D22 R23 Y24 H25 R26 N30 W31 R32 K33 K35 G36 I37 D38 R42 R44 F45 R46 P52 K53 I54 G55 G57 S58 N59 K60 F64 P67 N77 E94 A96 H97 N98 S100 A101 N103 R104 K117 N120 G123 R124

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6n8j, PDBe:6n8j, PDBj:6n8j
• PDBsum: 6n8j
• PubMed: 30814529
• UniProt: P38061|RL32_YEAST Large ribosomal subunit protein eL32 (Gene Name=RPL32)