Structure of PDB 4v6o Chain AO Binding Site BS01

Receptor Information

>4v6o Chain AO (length=123) Species: 562 (Escherichia coli)

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRK
VCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGA
LDCSGVKDRKQARSKYGVKRPKA

Ligand information

>4v6o 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: 4v6o Structural characterization of mRNA-tRNA translocation intermediates.
• Resolution: 14.7 Å
• Binding residue (original residue number in PDB): A1 T2 N4 Q5 R8 K9 R11 A12 R13 K14 A16 K17 S18 N19 V20 A22 C26 P27 Q28 R35 Y37 P41 K42 K43 P44 N45 S46 R49 R53 T57 F60 Y65 G67 G68 E69 G70 R82 G83 R85 V86 K87 D88 L89 G91 R93 G99 A100 K107 D108 R109 K110 Q111 A112 R113 S114 K115 Y116 R120 K122 A123
• Binding residue (residue number reindexed from 1): A1 T2 N4 Q5 R8 K9 R11 A12 R13 K14 A16 K17 S18 N19 V20 A22 C26 P27 Q28 R35 Y37 P41 K42 K43 P44 N45 S46 R49 R53 T57 F60 Y65 G67 G68 E69 G70 R82 G83 R85 V86 K87 D88 L89 G91 R93 G99 A100 K107 D108 R109 K110 Q111 A112 R113 S114 K115 Y116 R120 K122 A123

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0034336 misfolded RNA binding

Biological Process

• GO:0000372 Group I intron splicing
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0033120 positive regulation of RNA splicing
• GO:0034337 RNA folding
• 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

External links

• PDB: RCSB:4v6o, PDBe:4v6o, PDBj:4v6o
• PDBsum: 4v6o
• PubMed: 22467828
• UniProt: P0A7S3|RS12_ECOLI Small ribosomal subunit protein uS12 (Gene Name=rpsL)