Structure of PDB 6fyy Chain f Binding Site BS01

Receptor Information

>6fyy Chain f (length=74) Species: 284590 (Kluyveromyces lactis NRRL Y-1140)

GKKRKKKVYTTPKKIRHKHKKVKLAVLNYYKVDDEGKVAKLRKECPNCGP
GIFLANHGDRFYCGKCHSTFATQK

Ligand information

>6fyy Chain 2 (length=1780)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacauggauaucug
ugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagag
auguauuuauuagauaaaaaaucaaugucuucggacuccuugaugauuca
uaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaa
uuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuc
aacggguaacggggaauaaggguucgauuccggagagggagccugagaaa
cggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccua
auucagggagguagugacaauaaauaacgauacagggcccauucgggucu
uguaauuggaaugaguacaauguaaauaccuuaacgaggaacaacuggag
ggcaagucuggugccagcagccgcgguaauuccagcuccaguagcguaua
uuaaaguuguugcaguuaaaaagcucguaguugaacuuugggucugguug
uccggucgguuuuucaaccggaucuuuccuucuggcuaaccuguacuccu
ugugggugcaggcgaaccaggacuuuuacuuugaaaaaauuagaguguuc
aaagcaggcgaaagcucgaauauauuagcauggaauaauggaauaggacg
uuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggga
cggucgggggcaucaguauucaauugucagaggugaaauucuuggauuua
uugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaauc
aagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuua
accauaaacuaugccgacuagggaucgggugguguuuuucuuaugaccca
cucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaugg
ucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagug
gagccugcggcuuaauuugacucaacacggggaaacucaccagguccaga
cacaauaaggauugacagauugagagcucuuucuugauuuuguggguggu
ggugcauggccguucuuaguugguggagugauuugucugcuuaauugcga
uaacgaacgagaccuuaaccuacuaaauaggguugcuggcacuugccggu
ugacucuucuuagagggacuaucgguuucaagccgauggaaguuugaggc
aauaacaggucugugaugcccuuagacguucugggccgcacgcgcgcuac
acugacggagccagcgaguacaaccuuggccgagaggucuggguaaucuu
gugaaacuccgucgugcuggggauagagcauuguaauuauugcucuucaa
cgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacguccc
ugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuuagug
aggccucaggauuugcuuagagaagggggcaacuccaucucagagcgaag
aaucuggucaaacuuggucauuuagaggaacuaaaagucguaacaagguu
uccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fyy Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
• Resolution: 3.02 Å
• Binding residue (original residue number in PDB): G77 K78 R80 Y85 T87 P88 K89 K90 I91 R92 H93 H95 K97 K99 L100 Y105 R118 F129 A131 N132 H133 R136 Y138 G140 K141 H143 T145
• Binding residue (residue number reindexed from 1): G1 K2 R4 Y9 T11 P12 K13 K14 I15 R16 H17 H19 K21 K23 L24 Y29 R42 F53 A55 N56 H57 R60 Y62 G64 K65 H67 T69

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0031386 protein tag activity
• GO:0031625 ubiquitin protein ligase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0016567 protein ubiquitination
• GO:0019941 modification-dependent protein catabolic process

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6fyy, PDBe:6fyy, PDBj:6fyy
• PDBsum: 6fyy
• PubMed: 30475211
• UniProt: P69061|RS27A_KLULA Ubiquitin-ribosomal protein eS31 fusion protein (Gene Name=ubi3)