Structure of PDB 6zqd Chain Db Binding Site BS01

Receptor Information

>6zqd Chain Db (length=81) Species: 559292 (Saccharomyces cerevisiae S288C)

VLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQ
TAVTCESCSTILCTPTGGKAKLSEGTSFRRK

Ligand information

>6zqd Chain D3 (length=1409)

ucugguugauccugccaguagucauaugcuugucucaaagauuaagccau
gcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucauu
aaaucaguuaucguuuauuugauaguuccuuacaugguauaacuguggua
auucuagagcuaauacaugcuaucucgacccuuuggaagagauguauuua
uuagauaucuucggacugaugauucauaauaacuuuucgaaucgcauggc
cuugugcuggcgaugguucauucaaauuucugcccuaucaacuuucgaug
guaggauaguggccuaccaugguuucaacggguaacggggaauaaggguu
cgauuccggagagggagccugagaaacggcuaccacauccaaggaaggca
gcaggcgcgcaaauuacccaauccuaauucagggagguagugacaauaaa
uaacgauacagggcccauucgggucuuguaauuggaaugaguacaaugua
aauaccuuaacgaggaacaauuggagggcaagucuggugccagcagccgc
gguaauuccagcuccaauagcguauauuguuguugcaguuaaaaagcucg
uaguugaacuggcccgguuggccggucggauuuccaacggggccuuuccu
ucuggcuaaccuugaguccuuguggcucuuggcgaaccaguuacuuugaa
aaaauuagaguguucaaagcaggcguauugcucgauauauuagcauggaa
uaauaguaggagguucuauucuaggaccaucguauuaauagggacggucg
ggggcaucaguauucaauugucagaggugaaauucuuggauuuauugaag
acuaacuacugcgaaagcauuugccaaggacguuuucauuaaucaagaac
gaaaguuaggggaucgaagaugaucagauaccgucguagucuuaaccaua
aacuaugccgacuagggaucgggugguguuuuuuuaaugacccacucggc
accuuacgagaaaucaaagucuuuggguucugggggaguauggucgcaag
gcuaaaaaaggaauugacggaagggcaccaccaggaguggagccugcggc
gcgcuacacugacggagccagcgagaccuuggccgagaggucuugggaaa
cuccgucgugcuggggauagagcauuguaauuauugcucuucaacgagga
auuccuaguaagcgcaagucaucagcuugcguugauuacgucccugcccu
uuguacacaccgcccgucgcuaguaccgauugaauggcuuagugaggccu
caggaucugcuuagagaagggggcaacuccaucucagagcggagauuugg
acaaacuuggucauuugaggaacuaauuccguaggugaaccugcggaagg
aucauuaaa

.<<<<<.......>>>>>.....<<<<<<...<.<..........<<<.<
<<..<<....<<....<<..........>>...>>.>>......<<....
....<<<..<<..<<....<<<..............<<....<<.<<...
....>>.>>.....>>.....<<<<<..<<....>>..>>>>><...<<<
<<<....<<....>>.<<......>>>>>>>>.....>...<<<<..<<<
.....>>>.>>>>....>>>...>>>>..>>>.<<<....<<<....<<<
<<<<<.......>>>>>>>>>>>......>>>...<<<.<<<<....>>>
>....>>>.>>.<<.<<<..........>>>.>>.<.<<<..>>>.>...
>>>>>>.........<<<....<<<.....>>>..>>>.......>.>..
...<<<<<<<.<<<<<....>>>>>.>>>.>>>>......<<..<.....
......>..>>.........<<<<<<.......<<<....>>>.......
...........>>>>>>..>>>>>>..........<<<((.....<.<<.
..<<<.<<..<<<<<.<<<<<.....<>.....>>>>>.>>>>>..<<<<
.<<<<.<..<<..<<<<<.....>>>>>..>>..>.>>>><<<<<.<<..
.....<<..<<.......>>.<<<.....>>>...>>......>>.>>..
>>>....>>>>.<<.<<<...>>>.>>.......>>....<<<<<<.<<.
..<<<<..<<..<<<<<<.<...<<<..(...>>>......>.>>>>>>.
.>>.......<<....>>...>>>>...>>>>>.>>>...>>>...>>.>
....<<<<<<....<...<<<<..)......>>>>...>.>>>>>>....
......<<<.<<.<<<..<<<<<<<<.<<<........>>>>>>>>>>>.
.>>>...<<..))>>...>>.....>>>.>>>..................
...............<<<<<<<<<<<<..<<.<<<<<<..<<<.<<<.>>
>.>>>.....<<<<<<<.........<<..<<<<....>>>>..>>....
>>>>>>>...........<<<<<<.<<....>>.>>>>>>..........
>>>>>>....<<<<<<<.........>>>>>>>......>>...>>>>>>
>............>>>>>..<<<<.<<....<<<<<<<<.<<<..<.<<.
.<...<<<<<<<.<<<<.<<<......>>>.>>>>.>>>>>>>..>..>>
.>..>>>.>>>>>>>>..>>.>>>>.<<<<<<<<<....>>>>>>>>>..
.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zqd 90 S pre-ribosome transformation into the primordial 40 S subunit.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): R17 H19 K20 K22 Q26 P28 S30 H49 Q51 P66 G68 G69 K70
• Binding residue (residue number reindexed from 1): R16 H18 K19 K21 Q25 P27 S29 H48 Q50 P65 G67 G68 K69

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zqd, PDBe:6zqd, PDBj:6zqd
• PDBsum: 6zqd
• PubMed: 32943521
• UniProt: P35997|RS27A_YEAST Small ribosomal subunit protein eS27A (Gene Name=RPS27A)