Structure of PDB 6fyx Chain p Binding Site BS01

Receptor Information

>6fyx Chain p (length=647) Species: 559292 (Saccharomyces cerevisiae S288C)

EFNFDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATG
KTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSPSS
SLKSWLMDDKVRDQFVLQDDVKTSVFWNSMFNEEDSLVESRENWSTNYVR
FSPKGTYLFSYHQQGVTAWGGPNFDRLRRFYHPDVRNSSVSPNEKYLVTF
STEPIIVEEDNEFSPFTKKNEGHQLCIWDIASGLLMATFPVIKSPYLKWP
LVRWSYNDKYCARMVGDSLIVHDATKNFMPLEAKALKPSGIRDFSFAPEG
VKLQPFRNGDEPSVLLAYWTPETNNSACTATIAEVPRGRVLKTVNLVQVS
NVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPVEKVELKD
SVFEFGWEPHGNRFVTISVHEVADMNYAIPANTIRFYAPETKEKTDVIKR
WSLVKEIPKTFANTVSWSPAGRFVVVGALVGPNMRRSDLQFYDMDYPGEK
NINDNNDVSASLKDVAHPTYSAATNITWDPSGRYVTAWSSSLKHKVEHGY
KIFNIAGNLVKEDIIAGFKNFAWRPRPSILSNAERKKVRKNLREWSAQFE
EQDAMEADTAMRDLHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQP

Ligand information

>6fyx 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: 6fyx Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): N412 T458 K459 S460 K462 T463
• Binding residue (residue number reindexed from 1): N325 T371 K372 S373 K375 T376

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003743 translation initiation factor activity
• GO:0005515 protein binding
• GO:0031369 translation initiation factor binding
• GO:0042802 identical protein binding

Biological Process

• GO:0001732 formation of cytoplasmic translation initiation complex
• GO:0002183 cytoplasmic translational initiation
• GO:0006412 translation
• GO:0006413 translational initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005852 eukaryotic translation initiation factor 3 complex
• GO:0010494 cytoplasmic stress granule
• GO:0016282 eukaryotic 43S preinitiation complex
• GO:0033290 eukaryotic 48S preinitiation complex
• GO:0043614 multi-eIF complex

External links

• PDB: RCSB:6fyx, PDBe:6fyx, PDBj:6fyx
• PDBsum: 6fyx
• PubMed: 30475211
• UniProt: P06103|EIF3B_YEAST Eukaryotic translation initiation factor 3 subunit B (Gene Name=PRT1)