Structure of PDB 4v65 Chain AS Binding Site BS01

Receptor Information

>4v65 Chain AS (length=150) Species: 562 (Escherichia coli)

ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK

Ligand information

>4v65 Chain A1 (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: 4v65 The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading
• Resolution: 9.0 Å
• Binding residue (original residue number in PDB): N18 R19 V20 S21 K22 T23 V24 K25 R28 Y49 K51 A52 R53 K61 K65 R68 K85 V87 T89 R92 Q96 P97 S99 G101 T102 A106 G107 G108 A109 R111 L123 A124 K125 Y127 S129 N131 I133 N134 R137
• Binding residue (residue number reindexed from 1): N10 R11 V12 S13 K14 T15 V16 K17 R20 Y41 K43 A44 R45 K53 K57 R60 K77 V79 T81 R84 Q88 P89 S91 G93 T94 A98 G99 G100 A101 R103 L115 A116 K117 Y119 S121 N123 I125 N126 R129

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:4v65, PDBe:4v65, PDBj:4v65
• PDBsum: 4v65
• UniProt: P0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)