Structure of PDB 8cgr Chain K Binding Site BS01

Receptor Information

>8cgr Chain K (length=117) Species: 679895 (Escherichia coli BW25113)

RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFA
AQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITD
VTPIPHDGCRPPKKRRV

Ligand information

>8cgr Chain A (length=1060)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggccucuugccaucggaugugcccagaugggauuagcuaguagguggg
guaacggcucaccuaggcgacgaucccuagcuggucugagaggaugacca
gccacacuggaacugagacacgguccagacuccuacgggaggcagcagug
gggaauauugcacaaugggcgcaagccugaugcagccaugccgcguguau
gaagaagcccuucggguuguaaaguacuuucagcggggaggaagggagua
aaguuaauaccuuugcucauugacguuacccgcagaagaagcaccggcua
acuccgugccagcagccgcgguaauacggagggugcaagcguuaaucgga
auuacugggcguaaagcgcacgcaggcgguuuguuaagucagaugugaaa
uccccgggcucaaccugggaacugcaucugauacuggcaagcuugagucu
cguagagggggguagaauuccagguguagcggugaaaugcguagagaucu
ggaggaauaccgguggcgaaggcggcccccuggacgaagacugacgcuca
ggugcgaaagcguggggagcaaacaggauuagauacccugguaguccacg
ccguaaacgaugucgacuuggagguugugccggcguggcuuccggagcua
acgcguuaagucgaccgccuggggaguacggccgcaagguuaaaacucaa
augaauugacggggguuguacacaccgcccgucacaccaugggagugggu
ugcaaaagaaguagguagcuuaaccuucgggagggcgcuuaccacuuugu
gauucaugacuggggugaagucguaacaagguaaccguaggggaaccugc
gguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cgr Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 2.12 Å
• Binding residue (original residue number in PDB): H22 N28 N29 I31 T33 G39 N40 A41 W44 T46 G48 G49 R53 G54 S55 K57 K87 P115 I116 P117 H118 X119 G120 C121 R122 P123 P124 K125 R127 R128
• Binding residue (residue number reindexed from 1): H10 N16 N17 I19 T21 G27 N28 A29 W32 T34 G36 G37 R41 G42 S43 K45 K75 P103 I104 P105 H106 X107 G108 C109 R110 P111 P112 K113 R115 R116

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8cgr, PDBe:8cgr, PDBj:8cgr
• PDBsum: 8cgr
• PubMed: 37550453
• UniProt: P0A7R9|RS11_ECOLI Small ribosomal subunit protein uS11 (Gene Name=rpsK)