Structure of PDB 6yam Chain P Binding Site BS01

Receptor Information

>6yam Chain P (length=150) Species: 9986 (Oryctolagus cuniculus)

GRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIG
VILRDSHGVAQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKH
LERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWKYESSTASALVA

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): G2 R3 M4 K9 G10 L11 S12 S14 A15 S48 R55 Q62 R64 K70 R73 D87 H90 K94 H101 R104 N105 K107 D108 K109 D110 K112 F113 R114 L117 S120 R121 R124 R127 Y128
• Binding residue (residue number reindexed from 1): G1 R2 M3 K8 G9 L10 S11 S13 A14 S47 R54 Q61 R63 K69 R72 D86 H89 K93 H100 R103 N104 K106 D107 K108 D109 K111 F112 R113 L116 S119 R120 R123 R126 Y127

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6yam, PDBe:6yam, PDBj:6yam
• PDBsum: 6yam
• UniProt: G1SP51|RS13_RABIT Small ribosomal subunit protein uS15 (Gene Name=RPS13)