Structure of PDB 8p16 Chain j Binding Site BS01

Receptor Information

>8p16 Chain j (length=156) Species: 562 (Escherichia coli)

ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK
SVEEIL

Ligand information

>8p16 Chain 2 (length=1536)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaauucuuugcugacgaguggc
ggacgggugaguaaugucugggaaacugccugauggagggggauaacuac
uggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagggggac
cuucgggccucuugccaucggaugugcccagaugggauuagcuaguaggu
gggguaacggcucaccuaggcgacgaucccuagcuggucugagaggauga
ccagccacacuggaacugagacacgguccagacuccuacgggaggcagca
guggggaauauugcacaaugggcgcaagccugaugcagccaugccgcgug
uaugaagaaggccuucggguuguaaaguacuuucagcggggaggaaggga
guaaaguuaauaccuuugcucauugacguuacccgcagaagaagcaccgg
cuaacuccgugccagcagccgcgguaauacggagggugcaagcguuaauc
ggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucagaugug
aaauccccgggcucaaccugggaacugcaucugauacuggcaagcuugag
ucucguagagggggguagaauuccagguguagcggugaaaugcguagaga
ucuggaggaauaccgguggcgaaggcggcccccuggacgaagacugacgc
ucaggugcgaaagcguggggagcaaacaggauuagauacccugguagucc
acgccguaaacgaugucgacuuggagguugugcccuugaggcguggcuuc
cggagcuaacgcguuaagucgaccgccuggggaguacggccgcaagguua
aaacucaaaugaauugacgggggcccgcacaagcgguggagcaugugguu
uaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacggaag
uuuucagagaugagaaugugccuucgggaaccgugagacaggugcugcau
ggcugucgucagcucguguugugaaauguuggguuaagucccgcaacgag
cgcaacccuuauccuuuguugccagcgguccggccgggaacucaaaggag
acugccagugauaaacuggaggaagguggggaugacgucaagucaucaug
gcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaagaga
agcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccgga
uuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgugg
aucagaaugccacggugaauacguucccgggccuuguacacaccgcccgu
cacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucggga
gggcgcuuaccacuuugugauucaugacuggggugaagucguaacaaggu
aaccguaggggaaccugcgguuggaucaccuccuua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p16 The compensatory mechanism of a naturally evolved E167K RF2 counteracting the loss of RF1 in bacteria
• Resolution: 2.77 Å
• Binding residue (original residue number in PDB): V21 S22 K23 T24 V25 K26 G27 R29 Y50 K52 R54 K62 R69 H89 T90 F95 A99 S100 T103 I106 A107 G108 R112 L124 A125 K126 Y128 S130 T131 N132 N135 R138
• Binding residue (residue number reindexed from 1): V12 S13 K14 T15 V16 K17 G18 R20 Y41 K43 R45 K53 R60 H80 T81 F86 A90 S91 T94 I97 A98 G99 R103 L115 A116 K117 Y119 S121 T122 N123 N126 R129

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic
• GO:1990145 maintenance of translational fidelity

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:8p16, PDBe:8p16, PDBj:8p16
• PDBsum: 8p16
• UniProt: P0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)