Structure of PDB 8k4e Chain Q Binding Site BS01

Receptor Information

>8k4e Chain Q (length=80) Species: 83333 (Escherichia coli K-12)

KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNEC
GIGDVVEIRECRPLSKTKSWTLVRVVEKAV

Ligand information

>8k4e Chain A (length=1426)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccugguaaccgua
ggggaaccugcgguuggaucaccucc

........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<......
.....<<<..<<<..<<.<...<<<<<<<<........>>>>>.>>>.>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<...
..<<<<<......>>>>>......>>.>.....<<<....>>>....<<<
<<<..<......>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<.
.<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....
>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>
...>>>............<<<...<.<<<....>>>..>>>>.....>>>
>>>..<<<<.......<<<<..>>>>......>>>>...<.<<<<<....
..<<<<<<<<<<.......>>>>>>>>.>>.......>>>>>....>..<
<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>
>>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<
<<<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>
>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>.
.....>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>
>...>>>...>>>>....<<<<<<...<<...<<<<.........>>>>.
..>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>
>>>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<<...
.>>>>....>>>..)))).]<<<....<<<<<<.<<.<<<<<...<<<<<
<<<........<<........>>..........<<<<<<<......<<<<
<<<..<<<<<<<....>>>>>>>...<<....>>..>>>>>.>>.<<<.<
<<..<<<<<<.......<<<<<<<<<....>>>...<<<......>>>..
.>>>>>>.....<<<<.<<<<<<<...<...<<<.....>>>.>....>>
>>>>>.....<<<<<.....>>>>>........>>>>.........>>>.
..>>>>>>>>>...>>>>>>>......>>>>>>>>.....<<<<<<<...
..<<<..<<...<<<....>>>...>>....>>>.....>>>>>>>....
..<....<<<<<<<........>>>>>>>....>......>>>>>....<
<<<<<<.........>>>>>>>......>>...>>>>>>.....<<<<<<
<<....>>>>>>>>....>>>.....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8k4e Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex-II
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R6 S14 K16 M17 E18 F28 K36 F37 R40 T42 K43 H45 E63 R65 P66 S68 K69 T70 K71 W73
• Binding residue (residue number reindexed from 1): R3 S11 K13 M14 E15 F25 K33 F34 R37 T39 K40 H42 E60 R62 P63 S65 K66 T67 K68 W70

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

Cellular Component

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

External links

• PDB: RCSB:8k4e, PDBe:8k4e, PDBj:8k4e
• PDBsum: 8k4e
• UniProt: P0AG63|RS17_ECOLI Small ribosomal subunit protein uS17 (Gene Name=rpsQ)