Structure of PDB 6yam Chain J Binding Site BS01

Receptor Information

>6yam Chain J (length=190) Species: 9986 (Oryctolagus cuniculus)

SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVG
GGRKAIIIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKP
TRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLI
KVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL

Ligand information

>6yam Chain 2 (length=1743)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcuacuuggauaacugugguaauuc
uagagcuaauacaugccgacggcgcugacucccuuugugugggaugcgug
cauuuaucagaucaaaaccaacccggucggcggcuuuggugacucuagau
aaccucgggccgaucgcagcccuccguggcggcgacgacccauucgaacg
ucugcccuaucaacuuucgaugguagucgccgugccuaccauggugacca
cgggugacggggaaucaggguucgauuccggagagggagccugagaaacg
gcuaccacauccaaggaaggcagcaggcgcgcaaauuacccacucccgac
ccggggagguagugacgaaaaauaacaauacaggacucuuucgaggcccu
guaauuggaaugaguccacuuuaaauccuuuaacgaggauccauuggagg
gcaagucuggucgcagcagccgcgguaauuccagcuccaauagcguauau
uaaaguugcugcaguuaaaaagcucguaguuggaucuuguggaggguucc
ccgccccuugccucucggcgccggcccgaagcguuuacuuugaaaaaauu
agaguguucaaagcaggcccgagccgccuggauaccgcagcuaggaauaa
uggaauaggaccgcgguucuauuuuguugguuuucggaacugaggccaug
auuaagagggacggccgggggcauucguauugcgccgcuagaggugaaau
ucuuggaccggcgcaagacggaccagagcgaaagcauuugccaagaaugu
uuucauuaaucaagaacgaaagucggagguucgaagacgaucagauaccg
ucguaguuccgaccauaaacgaugccgacuggcgaugcggcggcguuauu
cccaugacccgccgggcagcuuccgggaaaccaaagucuuuggguuccgg
ggggaguaugguugcaaagcugaaacuuaaaggaauugacggaagggcac
caccaggaguggagccugcggcuuaauuugacucaacacgggaaaccuca
cccggcccggacacggacaggauugacagauugauagcucuuucucgauu
cugugggugguggugcauggccguucuuaguugguggagcgauuugucug
guuaauuccgauaacgaacgagacucuggcaugcuaacuaguuacgcgac
ccccgagcggucggcgucccccaacuucuuagagggacaaguggcguuca
gccacccgagauugagcaauaacaggucugugaugcccuuagaugucggg
gcugcacgcgcgcuacacugacuggcucagcgugugccuacccuacgccg
gcaggcgcggguaacccguugaaccccauucgugauggggaucggggauu
gcaauuauuccccaugaacgaggaauucccaguaagugcgggucauaagc
uugcguugauuaagucccugcccuuuguacacaccgcccgucgcuacuac
cgauuggaugguuuagugaggcccucggaucggcccgccggggugcccug
gcggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaag
ucguaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yam Structural Insights into the Mammalian Late-Stage Initiation Complexes.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): R98 R99 I100 K103 R106 S108 R109 T110 K111 N112 Q114 K115 P117 R118 S119 R120 T121 L122 T123
• Binding residue (residue number reindexed from 1): R94 R95 I96 K99 R102 S104 R105 T106 K107 N108 Q110 K111 P113 R114 S115 R116 T117 L118 T119

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005813 centrosome
• GO:0005840 ribosome
• GO:0005856 cytoskeleton
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6yam, PDBe:6yam, PDBj:6yam
• PDBsum: 6yam
• UniProt: G1SVB0|RS7_RABIT Small ribosomal subunit protein eS7 (Gene Name=RPS7)