Structure of PDB 4v5h Chain AL Binding Site BS01

Receptor Information

>4v5h Chain AL (length=123) Species: 562 (Escherichia coli)

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRK
VCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGA
LDCSGVKDRKQARSKYGVKRPKA

Ligand information

>4v5h 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: 4v5h Structural insight into nascent polypeptide chain-mediated translational stalling.
• Resolution: 5.8 Å
• Binding residue (original residue number in PDB): T2 N4 Q5 R8 K9 R11 A12 R13 K14 K17 N19 E24 C26 P27 Q28 R30 K42 N45 S46 L48 R49 K50 N58 Y65 G67 G68 E69 R82 V86 K87 P90 R93 R109 K110 Q111 A112 R113 S114 K115 Y116 V118 K119 R120
• Binding residue (residue number reindexed from 1): T2 N4 Q5 R8 K9 R11 A12 R13 K14 K17 N19 E24 C26 P27 Q28 R30 K42 N45 S46 L48 R49 K50 N58 Y65 G67 G68 E69 R82 V86 K87 P90 R93 R109 K110 Q111 A112 R113 S114 K115 Y116 V118 K119 R120

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:4v5h, PDBe:4v5h, PDBj:4v5h
• PDBsum: 4v5h
• PubMed: 19933110
• UniProt: P0A7S3|RS12_ECOLI Small ribosomal subunit protein uS12 (Gene Name=rpsL)