Structure of PDB 4v6d Chain AE Binding Site BS01

Receptor Information

>4v6d Chain AE (length=150) Species: 83333 (Escherichia coli K-12)

ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK

Ligand information

>4v6d Chain AA (length=1533)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuu
cgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaac
aagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6d Structures of the ribosome in intermediate States of ratcheting.
• Resolution: 3.814 Å
• Binding residue (original residue number in PDB): V20 S21 K22 T23 V24 K25 R28 Y49 K51 R53 K61 E64 K65 H88 T89 R92 K125 I133 N134
• Binding residue (residue number reindexed from 1): V12 S13 K14 T15 V16 K17 R20 Y41 K43 R45 K53 E56 K57 H80 T81 R84 K117 I125 N126

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

External links

• PDB: RCSB:4v6d, PDBe:4v6d, PDBj:4v6d
• PDBsum: 4v6d
• PubMed: 19696352
• UniProt: P0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)