Structure of PDB 4v78 Chain AK Binding Site BS01

Receptor Information

>4v78 Chain AK (length=117) Species: 83333 (Escherichia coli K-12)

RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFA
AQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITD
VTPIPHNGCRPPKKRRV

Ligand information

>4v78 Chain AA (length=1530)

ugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaacac
augcaagucgaacgguaacaggaagaagcuugcuucuuugcugacgagug
gcggacgggugaguaaugucugggaaacugccugauggagggggauaacu
acuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagaggggg
accuucgggccucuugccaucggaugugcccagaugggauuagcuaguag
gugggguaacggcucaccuaggcgacgaucccuagcuggucugagaggau
gaccagccacacuggaacugagacacgguccagacuccuacgggaggcag
caguggggaauauugcacaaugggcgcaagccugaugcagccaugccgcg
uguaugaagaaggccuucggguuguaaaguacuuucagcggggaggaagg
gaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagcacc
ggcuaacuccgugccagcagccgcgguaauacggagggugcaagcguuaa
ucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucagaug
ugaaauccccgggcucaaccugggaacugcaucugauacuggcaagcuug
agucucguagagggggguagaauuccagguguagcggugaaaugcguaga
gaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacugac
gcucaggugcgaaagcguggggagcaaacaggauuagauacccugguagu
ccacgccguaaacgaugucgacuuggagguugugcccuugaggcguggcu
uccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaaggu
uaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaugugg
uuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacgga
aguuuucagagaugagaaugugccuucgggaaccgugagacaggugcugc
auggcugucgucagcucguguugugaaauguuggguuaagucccgcaacg
agcgcaacccuuauccuuuguugccagcgguccggccgggaacucaaagg
agacugccagugauaaacuggaggaagguggggaugacgucaagucauca
uggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaaga
gaagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccg
gauuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgu
ggaucagaaugccacggugaauacguucccgggccuuguacacaccgccc
gucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucgg
gagggcgcuuaccacuuugugauucaugacuggggugaagucguaacaag
guaaccguaggggaaccugcgguuggauca

....<<<<....((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<
.<<<..<<<..<<.<<..<<<<<<<..........>>>>.>>>>>..>>>
>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<.....<<
<<<<....>>>>>>......>>.>.....<<<....>>>....<<<<<<.
.<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<...<<
<<<<.........>>>>>>.>>>......>>>..<<<<<<<<....>>>>
...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>...>
>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>>>>.
.<<<<.......<<<....>>>......>>>>...<.<<<<<........
<<<<<<.<.......>.>>>>>>..........>>>>>....>..<<<<<
(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>>>>>
>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<
<....<.<<<<<<.....>>>>>>.>..>>>>>>>>..>>>>>>>>>...
<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>.....
.>>>>>>>>...........<<....>>.>>>>>>>..>>>.>>>>>...
>>>...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>...>>
>>>>>>..........<<<<<<..<<<<<<<<<<<<.....>>>>>>>>>
>>>...<<..))>>.....>>>>>>.>>>.<<<......<<<<....>>>
>....>>>..))))..<<<<<.<<<<<<<.<....<<<<...<<<<<<<<
.......<<........>>..........<<<<<<<......<<<<<<<.
.<<<<<<<....>>>>>>>...<<....>>..>>>>>.>>.<<<.<<<..
<<<<<<<......<<<<<<<<<....>>>..<<<<......>>>>..>>>
>>>.....<<<<.<<<<<<....<<..<<<.....>>>>>.....>>>>>
>.....<<<<<.....>>>>>........>>>>.......>.>>>...>>
>>>>>>>...>>>>>>>....>.>>>>>>>......<<<<<<<.....<<
<..<<...<<<....>>>...>>....>>>.....>>>>>>>........
...<<<<<<<........>>>>>>>..........>>>>......<<<<<
<<.........>>>>>>>.......>...>>>>>>>>>>.>>.......<
<.<.<<<<.<<<..<<<<<<<<<<<<....<<<<<<.<<<...<<....>
>..>>>>>>>>>...>>>>>>>>>>>>..>>>.>>>>..>.>>.......
..<<<<<<<<<....>>>>>>>>>......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v78 Energy barriers and driving forces in tRNA translocation through the ribosome.
• Resolution: 20.0 Å
• Binding residue (original residue number in PDB): H21 N27 N28 T32 G38 N39 A40 W43 T45 G47 G48 K124 R126 R127 V128
• Binding residue (residue number reindexed from 1): H10 N16 N17 T21 G27 N28 A29 W32 T34 G36 G37 K113 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:4v78, PDBe:4v78, PDBj:4v78
• PDBsum: 4v78
• PubMed: 24186064
• UniProt: P0A7R9|RS11_ECOLI Small ribosomal subunit protein uS11 (Gene Name=rpsK)