Structure of PDB 4v6l Chain AN Binding Site BS01

Receptor Information

>4v6l Chain AN (length=103) Species: 83333 (Escherichia coli K-12)

MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFT
VLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQI
SLG

Ligand information

>4v6l Chain AA (length=1542)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccu
ucgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaa
caagguaaccguaggggaaccugcgguuggaucaccuccuua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6l Structural insights into cognate versus near-cognate discrimination during decoding.
• Resolution: 13.2 Å
• Binding residue (original residue number in PDB): M1 Q2 N3 R7 R9 H15 R16 D19 R37 G38 P39 I40 P41 L42 P43 T44 R45 K46 E47 R48 F49 T50 I53 S54 P55 H56 V57 K59 D60 A61 R62 D63 Q64 Y65 R68 H70 L71 R72 L73 Q99 S101 L102 G103
• Binding residue (residue number reindexed from 1): M1 Q2 N3 R7 R9 H15 R16 D19 R37 G38 P39 I40 P41 L42 P43 T44 R45 K46 E47 R48 F49 T50 I53 S54 P55 H56 V57 K59 D60 A61 R62 D63 Q64 Y65 R68 H70 L71 R72 L73 Q99 S101 L102 G103

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0001072 transcription antitermination factor activity, RNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0031564 transcription antitermination
• GO:0032784 regulation of DNA-templated transcription elongation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0008023 transcription elongation factor complex
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6l, PDBe:4v6l, PDBj:4v6l
• PDBsum: 4v6l
• PubMed: 21378755
• UniProt: P0A7R5|RS10_ECOLI Small ribosomal subunit protein uS10 (Gene Name=rpsJ)