Structure of PDB 6vyu Chain K Binding Site BS01

Receptor Information
>6vyu Chain K (length=156) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK
SVEEIL
Ligand information
>6vyu Chain D (length=1524) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccggccagcagcccgguaauacggagggugcaagcguu
aaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucaga
ugugaaauccccgggcucaaccugggaacugcaucugauacuggcaagcu
ugagucucguagagggggguagaauuccagguguagcggugaaaugcgua
gagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacug
acgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggua
guccacgccguaaacgaugucgacuuggagguugugcccuugaggcgugg
cuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaag
guuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaugu
gguuuaauucgauaacgcgaagaaccuuaccuggucuugacauccacgga
aguuuucagagaugagaaugugccuucgggaaccgugagacaggugcugc
auggcugucgucagcucguguugugaaauguuggguuaagucccgcaacg
agcgcaacccuuauccuuuguugccagcgguccggccgggaacucaaagg
agacugccagugauaaacuggaggaagguggggaugacgucaagucauca
ugcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaagag
aagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccgg
auuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgug
gaucagaaugccacggugaauacguucccgggccuuguacacaccgccgu
acaccaugggaguggguugcaaaagaaguagguagcuuaaccuucgggag
ggcgcuuaccacuuugugauucaugacuggggugaagucgaacaagguaa
ccguaggggccugcgguuggauca
........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<<..<<<<<<<<<......>>>>>>.>>>>>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<...
..<<<<<......>>>>>......>>.>.....<<<....>>>....<<<
<<<..<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<.
.<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....
>>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>
...>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>
>>>..<<<<......<<<<....>>>>.....>>>>..<<.<<<<<....
..<.<<<<<<<<.......>>>>>>>>.>........>>>>>....>>.<
<<<<(((...<<<<<.......)))........>>>>>>>>>>..>>>>>
>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<
<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>>.
..<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>...
...>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>>.
..>>>...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>...
>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>>>
>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<<....>
>>>....>>>..)))).]<<<<<.<<<<<<<.<<.<<<<<<..<<<<<<<
<<<......<<......>>..........<<<<<<<......<<<<<<<.
.<<<<<<<....>>>>>>>...<......>..>>>>>.>>.<<<......
<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>..>>>
>>>.....<<<<.<<<<<<<...<<..<<<.....>>>>>....>>>>>>
>.....<<<<<.....>>>>>........>>>>.........>>>...>>
>..>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<.....<<<
..<<...<<<....>>>...>>....>>>.....>>>>>>>......<..
..<<<<<<<........>>>>>>>....>.....>>>>>>....<<<<<<
<.........>>>>>>>......>>...>>>>>>>>>>.>>......<<.
.<<<<.<<<..<<<<<<<<<<<<....<<<<<<.<<<<..<<<..>>>.>
>>>>>>>>>...>>>>>>>>>>>>..>>>.>>>>....>>........<<
<<<<<<<..>>>>>>>>>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6vyu Structural basis of transcription-translation coupling.
Resolution7.0 Å
Binding residue
(original residue number in PDB)		N19 V21 S22 K23 T24 V25 K26 G27 R29 Y50 K52 R54 K62 R69 H89 T90 R93 Q97 S100 T103 A107 G108 R112 L124 A125 K126 A127 Y128 S130 T131 N132 N135 R138
Binding residue
(residue number reindexed from 1)		N10 V12 S13 K14 T15 V16 K17 G18 R20 Y41 K43 R45 K53 R60 H80 T81 R84 Q88 S91 T94 A98 G99 R103 L115 A116 K117 A118 Y119 S121 T122 N123 N126 R129
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:6vyu, PDBe:6vyu, PDBj:6vyu
PDBsum6vyu
PubMed32820061
UniProtP0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)

[Back to BioLiP]