Structure of PDB 4v6y Chain BC Binding Site BS01

Receptor Information

>4v6y Chain BC (length=271) Species: 83333 (Escherichia coli K-12)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>4v6y 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: 4v6y Energy barriers and driving forces in tRNA translocation through the ribosome.
• Resolution: 12.0 Å
• Binding residue (original residue number in PDB): R174 R176
• Binding residue (residue number reindexed from 1): R174 R176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0032297 negative regulation of DNA-templated DNA replication initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990082 DnaA-L2 complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6y, PDBe:4v6y, PDBj:4v6y
• PDBsum: 4v6y
• PubMed: 24186064
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)