Structure of PDB 7uph Chain f Binding Site BS01

Receptor Information

>7uph Chain f (length=117) Species: 562 (Escherichia coli)

RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFA
AQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITD
VTPIPHNGCRPPKKRRV

Ligand information

>7uph Chain I (length=4438)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccag
ucaauaagucuugagcuaaccgguacuaaugaaccgugaggcuuaaccuu
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauguguaggauaggugggaggcuuugaaguguggacgccagucugcaug
gagccgaccuugaaauaccacccuuuaauguuugauguucuaacguugac
ccguaauccggguugcggacagugucugguggguaguuugacuggggcgg
ucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugguc
ggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgu
gacggcgcgagcaggugcgaaagcaggucauagugauccggugguucuga
auggaagggccaucgcucaacggauaaaagguacuccggggauaacaggc
ugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugu
cggcucaucacauccuggggcugaaguaggucccaaggguauggcuguuc
gccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguuc
ggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagu
acgagaggaccggaguggacgcaucacugguguucggguugucaugccaa
uggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucu
aagcacgaaacuugccccgagaugaguucucccugacccuuuaagggucc
ugaaggaacguugaagacgacgacguugauaggccggguguguaaggacg
accuucgggagggcgcuuaccacuuugugauucaugacuggggugaaguc
guaacaagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7uph Three-dimensional structure-guided evolution of a ribosome with tethered subunits.
• Resolution: 4.18 Å
• Binding residue (original residue number in PDB): H10 S14 N16 N17 T21 T23 Q26 G27 N28 A29 W32 T34 G36 G37 R41 G42 S43 K45 P103 I104 P105 H106 N107 G108 C109 R110 R115 R116 V117
• Binding residue (residue number reindexed from 1): H10 S14 N16 N17 T21 T23 Q26 G27 N28 A29 W32 T34 G36 G37 R41 G42 S43 K45 P103 I104 P105 H106 N107 G108 C109 R110 R115 R116 V117

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:7uph, PDBe:7uph, PDBj:7uph
• PDBsum: 7uph
• PubMed: 35836020
• UniProt: P0A7R9|RS11_ECOLI Small ribosomal subunit protein uS11 (Gene Name=rpsK)