Structure of PDB 6vwm Chain A Binding Site BS02

Receptor Information

>6vwm Chain A (length=271) Species: 562 (Escherichia coli)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>6vwm Chain 1 (length=1508)

agaguuugaucauggcucagauugaacgcuggcggcaggccuaacacaug
caagucgaacgguaacaggaagcuuugcugacgaguggcggacgggugag
uaaugucugggaaacugccugauggagggggauaacuacuggaaacggua
gcuaauaccgcauaacgucgcaagaccaaagagggggaccuucgggccuc
uugccaucggaugugcccagaugggauuagcuaguaggugggguaacggc
ucaccuaggcgacgaucccuagcuggucugagaggaugaccagccacacu
ggaacugagacacgguccagacuccuacgggaggcagcaguggggaauau
ugcacaaugggcgcaagccugaugcagccaugccgcguguaugaagaagg
ccuucggguuguaaaguacuuucagcggggaggaagggaguaaaguuaau
accuuugcucauugacguuacccgcagaagaagcaccggcuaacuccgug
ccagcagccgcgguaauacggagggugcaagcguuaaucggaauuacugg
gcguaaagcgcacgcaggcgguuuguuaagucagaugugaaauccccggg
cucaaccugggaacugcaucugauacuggcaagcuugagucucguagagg
gggguagaauuccagguguagcggugaaaugcguagagaucuggaggaau
accgguggcgaaggcggcccccuggacgaagacugacgcucaggugcgaa
agcguggggagcaaacaggauuagauacccugguaguccacgccguaaac
gaugucgacuuggagguugugcgcguggcuuccggagcuaacgcguuaag
ucgaccgccuggggaguacggccgcaagguuaaaacucaaaugaauugac
gggggcccgcacaagcgguggagcaugugguuuaauucgaugcaacgcga
agaaccuuaccuggucuugacauccacggaaguuuucagagaugagaaug
ugccuucgggaaccgugagacaggugcugcauggcugucgucagcucgug
uugugaaauguuggguuaagucccgcaacgagcgcaacccuuauccuuug
uugccagcgguccggccgggaacucaaaggagacugccagugauaaacug
gaggaagguggggaugacgucaagucaucauggcccuuacgaccagggcu
acacacgugcuacaauggcgcauacaaagagaagcgaccucgcgagagca
agcggaccucauaaagugcgucguaguccggauuggagucugcaacucga
cuccaugaagucggaaucgcuaguaaucguggaucagaaugccacgguga
auacguucccgggccuuguacacaccgcccgucacaccaugggagugggu
ugcaaaagaaguagguagcuuaaccuucgggagggcgcuuaccacuuugu
gauucaugacuggggugaagucguaacaagguaaccguagggaaaccugc
gguuggau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vwm mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): M200 R268
• Binding residue (residue number reindexed from 1): M200 R268

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:6vwm, PDBe:6vwm, PDBj:6vwm
• PDBsum: 6vwm
• PubMed: 32427100
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)