Structure of PDB 6wub Chain d Binding Site BS01

Receptor Information

>6wub Chain d (length=201) Species: 474186 (Enterococcus faecalis OG1RF)

SRYTGPSWKVSRRLGISLSGTGKELARRPYKPGQHGPNSRGKVSEYGMQL
TEKQKLRHMYGMNERQFRTLFIKASKIKEGKHGVNFMVLLEQRLDNVVYR
LGLATTRRQARQLVNHGHITVDGKRVDIPSYHVEVGQVIGVREKSQNIST
IKEAVEATVGRPAFVSFDTEKLEGSFTRLPERDELYPEIDEALVVEYYNQ
K

Ligand information

>6wub Chain a (length=1121)

ugagaguuugauccuggcucaggacgaacgcuggcggcgugccuaauaca
ugcaagucgaacgcuucuuggaaagaggaguggcggacgggugaguaaca
cguggguaaccuacccaucagagggggauaacacuuggaaacaggugcua
auaccgcauaacaguuuaugccgcauggcauaagagugaaaggcgcuuuc
gggugucgcugauggauggacccgcggugcauuagcuaguuggugaggua
acggcucaccaaggccacgaugcauagccgaccugagagggugaucggcc
acacugggacugagacacggcccagacuccuacgggaggcagcaguaggg
aaucuucggcaauggacgaaagucugaccgagcaacgccgcgugagugaa
gaagguuuucggaucguaaaacucuguuguuagagaagaacaaggacguu
aguaacugaacguccccugacgguaucuaaccagaaagccacggcuaacu
acgugccagcagccgcgguaauacguagguggcaagcguuguccggauuu
auugggcguaaagcgagcgcaggcgguuucuuaagucugaugugaaagcc
cccggcucaaccggggagggucauuggaaacugggagacuugagugcaga
agaggagaguggaauuccauguguagcggugaaaugcguagauauaugga
ggaacaccaguggcgaaggcggcucucuggucuguaacugacgcugaggc
ucgaaagcguggggagcaaacaggauuagauacccugguaguccacgccg
uaaacgaugagugcuaaguguuggaggguuuccgcccuucagugcugcag
caaacgcauuaagcacuccgccuggggaguacgaccgcaagguugaaacu
caaaggaauugacgggggcccgucagcucgugucgugagauguuggguua
agucccgcaacgagcgucccgggccuuguacacaccgcccgucacaccac
gagaguuuguaacacccgaagucggugagguaaccuuuuuggagccagcc
gccuaaggugggauagaugauuggggugaagucguaacaagguagccgua
ucggaaggugcggcuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wub Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): S2 R3 P7 W9 K10 R13 R14 R29 Y31 P33 G34 Q35 H36 S45 Q55 E65 R66 Q67 K77 T107 R109 Q110 Q113 N116 H117 H119 I129 S131
• Binding residue (residue number reindexed from 1): S1 R2 P6 W8 K9 R12 R13 R28 Y30 P32 G33 Q34 H35 S44 Q54 E64 R65 Q66 K76 T106 R108 Q109 Q112 N115 H116 H118 I128 S130

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6wub, PDBe:6wub, PDBj:6wub
• PDBsum: 6wub
• PubMed: 33004869
• UniProt: Q82ZI6|RS4_ENTFA Small ribosomal subunit protein uS4 (Gene Name=rpsD)