Structure of PDB 6vwl Chain d Binding Site BS01

Receptor Information
>6vwl Chain d (length=156) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGA
MRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS
VEEILG
Ligand information
>6vwl Chain 1 (length=1521) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaacac
augcaagucgaacgguaacaggaagcuuugcugacgaguggcggacgggu
gaguaaugucugggaaacugccugauggagggggauaacuacuggaaacg
guagcuaauaccgcauaacgucgcaagaccaaagagggggaccuucgggc
cucuugccaucggaugugcccagaugggauuagcuaguaggugggguaac
ggcucaccuaggcgacgaucccuagcuggucugagaggaugaccagccac
acuggaacugagacacgguccagacuccuacgggaggcagcaguggggaa
uauugcacaaugggcgcaagccugaugcagccaugccgcguguaugaaga
aggccuucggguuguaaaguacuuucagcggggaggaagggaguaaaguu
aauaccuuugcucauugacguuacccgcagaagaagcaccggcuaacucc
gugccagcagccgcgguaauacggagggugcaagcguuaaucggaauuac
ugggcguaaagcgcacgcaggcgguuuguuaagucagaugugaaaucccc
gggcucaaccugggaacugcaucugauacuggcaagcuugagucucguag
agggggguagaauuccagguguagcggugaaaugcguagagaucuggagg
aauaccgguggcgaaggcggcccccuggacgaagacugacgcucaggugc
gaaagcguggggagcaaacaggauuagauacccugguaguccacgccgua
aacgaugucgacuuggagguugugccgcguggcuuccggagcuaacgcgu
uaagucgaccgccuggggaguacggccgcaagguuaaaacucaaaugaau
ugacgggggcccgcacaagcgguggagcaugugguuuaauucgaugcaac
gcgaagaaccuuaccuggucuugacauccacggaaguuuucagagaugag
aaugugccuucgggaaccgugagacaggugcugcauggcugucgucagcu
cguguugugaaauguuggguuaagucccgcaacgagcgcaacccuuaucc
uuuguugccagcgguccggccgggaacucaaaggagacugccagugauaa
acuggaggaagguggggaugacgucaagucaucauggcccuuacgaccag
ggcuacacacgugcuacaauggcgcauacaaagagaagcgaccucgcgag
agcaagcggaccucauaaagugcgucguaguccggauuggagucugcaac
ucgacuccaugaagucggaaucgcuaguaaucguggaucagaaugccacg
gugaauacguucccgggccuuguacacaccgcccgucacaccaugggagu
ggguugcaaaagaaguagguagcuuaaccuucgggagggcgcuuaccacu
uugugauucaugacuggggugaagucguaacaagguaaccguagggaaac
cugcgguuggaucaccuccuu
....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<
.<<<..<<<..<<.<<..<<<<<<..>>>.>>>>>..>>>>>......<<
.......<<<<<<<..<<...<<<<<<<.<.<<.....<<<<<......>
>>>>......>>.>.....<<<....>>>....<<<<<<..<<....>>>
>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<..<<<<<<<......
...>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>
.<<<<<.<.........>>>>>>.<<<<<..>>>>>...>>>>>>.....
....<<<...<<<<<....>>>>.>>>>..>>.>>>>>>..<<<<.....
..<<<....>>>......>>>>..<<.<<<<<......<.<<<<<<<<..
.....>>>>>>>>.>........>>>>>....>>.<<<<<(((...<<<<
<.....<<.)))>>.......>>>>>>>>>>..>>>>>>>>>........
..<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<
<<<.....>>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<..
.<<<<<<<....<<<<<<<<...<<<......>>>......>>>>>>>>.
..........<<....>>.>>>>>>>..>>>.>>>>>...>>>...>>>>
....<<<<<<...<<...<<<<.........>>>>...>>>>>>>>....
......<<<<<<.<<<<<<<<<<<<.>>>>>>>>>>>>..<<..))>>..
...>>>>>>.>>>.<<<......<<<<....>>>>....>>>..)))).]
<<<<<.<<<<<<<.<<..<<<<<.<<<<<<<<<<<......<<.......
.>>..........<<<<<<<......<<<<<<<..<<<<<<<....>>>>
>>>....<....>...>>>>>.>>.<<<.<<<..<<<<<<.......<<<
<<<<<<....>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<
<<<<...<<..<<<.....>>>>>....>>>>>>>.....<<<<<.....
>>>>>........>>>>.........>>>...>>>>>>>>>...>>>>>>
>...>>.>>>>>>>>.>...<<<<<<<.....<<<..<<...<<<....>
>>...>>....>>>.....>>>>>>>......<....<<<<<<<......
..>>>>>>>....>.....>>>>>.....<<<<<<<.........>>>>>
>>......>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<
<<<<<<<<<<....<<<<<<.<<<<..<<....>>.>>>>>>>>>>...>
>>>>>>>>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>
>>>>>>>>.............
Receptor-Ligand Complex Structure
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PDB6vwl mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		V20 S21 T23 V24 R28 Y49 K51 K61 R68 T89 S99 A106 G107 K125 Y127 S129 N131 I133 N134 R137
Binding residue
(residue number reindexed from 1)		V11 S12 T14 V15 R19 Y40 K42 K52 R59 T80 S90 A97 G98 K116 Y118 S120 N122 I124 N125 R128
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
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:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vwl, PDBe:6vwl, PDBj:6vwl
PDBsum6vwl
PubMed32427100
UniProtP0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)

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