Structure of PDB 6s05 Chain g Binding Site BS01

Receptor Information

>6s05 Chain g (length=103) Species: 4932 (Saccharomyces cerevisiae)

AQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSAL
QGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIV
KKV

Ligand information

>6s05 Chain A (length=3146)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagaagacccuguugagcuugacucuaguuugacauugugaagaga
cauagaggguguagaauaagugggagcuucggcgccagugaaauaccacu
accuuuauaguuucuuuacuuauucaaugaagcggagacguucuagcauu
caaggucccauucggggcugauccggguugaagacauugucaggugggga
guuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagg
ggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccc
ccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccuau
cgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguuac
cacagggauaacuggcuuguggcagucaagcguucauagcgacauugcuu
uuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucggu
aagcguuggauuguucacccacuaauagggaacgugagcuggguuuagac
cgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauag
uaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuug
cggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaugg
cugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugc
uccacacaauauagauggauacgaauaaggcguccuuguggcgucgcuga
accauagcaggcuacgaauugcaaugucauuuugcguggggauaaaucau
uuguauacgacuuagauguacaacgggguauuguaagcaguagaguagcc
uuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6s05 Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): R4 V5 T6 R8 R9 R10 N11 P12 Y13 N14 T15 K21 K24 T25 P26 G27 R31 K37 L38 P42 Q52 G53 I54 S55 T56 R58 P59 R60 S66 K67 T68 K70 S73 R74 A75 Y76 G77 G78 R80 A82 N83 R88 R91 A92 I95 Q98
• Binding residue (residue number reindexed from 1): R3 V4 T5 R7 R8 R9 N10 P11 Y12 N13 T14 K20 K23 T24 P25 G26 R30 K36 L37 P41 Q51 G52 I53 S54 T55 R57 P58 R59 S65 K66 T67 K69 S72 R73 A74 Y75 G76 G77 R79 A81 N82 R87 R90 A91 I94 Q97

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6s05, PDBe:6s05, PDBj:6s05
• PDBsum: 6s05
• PubMed: 31115337
• UniProt: P87262|RL34A_YEAST Large ribosomal subunit protein eL34A (Gene Name=RPL34A)