Structure of PDB 4v4w Chain BN Binding Site BS02

Receptor Information

>4v4w Chain BN (length=114) Species: 562 (Escherichia coli)

SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIR
NRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLR
ERTGKAARIKERLN

Ligand information

>4v4w Chain B0 (length=2740)

cguacacgguggaugcccuggcagucaaggcgaugaaggacgugcuaauc
ugcgauaagcgucgguaaggugauaugaaccguuuaaccggcgauuuccg
aauggggaaccccgaucauuauccaaaugaggcgaaccgggggaacugaa
acaucuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagc
ggcgagcgaacggggagcagcccgagccuaaucaguguguguguugugga
agcgucuggaaaggcgcgcgauacagggugacagccccguacacaaugca
caugcuguagcucgaugaguagggcgggccgugguaccugucugaauaug
gggggaccauccuccaaggcuaaauacucugacugaccgauagugaacca
guaccgugagggaaaggcgaaaagaaccccggcgaggggagugaaaaaga
accugaaaccguguacguacaagcagugggaggcaccuuaugcguguuau
ggcgugccuuuuguauaaugggucagcgacuuauauucuguagcaagguu
aaccggggagccgaagggaaaccgagucuuaacgggcguuaaguugcagg
guauagacccgaaacccggugaucuagccaugggcagguugaagguuggg
uaacacuaacuggaggaccgaaccgacuaauguugaaaaauuagcggaug
acuuguggcugggggugaaaggccaaucaaaccgggagauagcugguucu
ccccgaaagcuauuuagguagcgccucgugaaucaucuccggggguagag
cacuguuucggcaagggggucgacuuccaacccgaugcaaacugcgaaua
ccggagauguuaucacgggagacacacggcggguguaacguccgucguga
agagggaaacaacccagaccgcagcuaaggucccaaagucaugguuaagu
gggaaacgaugugggaaggcccagacagccaggauguuggcuuagaagca
gccaucauuuaaagaaagcguaauagcucacuggucgagucggccugcgc
ggaagauguacggggcuaaaccaugcaccgaagcugcggcagcgacguua
ugcguuguuggguaggggagcguucuguagccugcgaaggugugcuguga
ggcaugcuggagguaucagaagugcgaaugcugacauaaguaacgauaaa
gcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaacguu
aaucggggcagggugagucgacccuaaggcgaggccgaaaggcguagucg
augggaaacagguuaauauuccuguacuuggugugugggugauggaggga
cggagaaggcuauguuaugccaagcuauggcugcugguugguacgcucaa
gggcgaucgggucagaaaaucuaccggucacaugccucagacguaucggg
agcuuccucggaagcgaaguaacaaagcccucuuccaggaaaagcuucua
aacguugaaacaugucaaaucguaccccaaaccgacacagguggucaggu
agagaauaccaggcgcuugagagaacucgggugaaggaacuaggcaaaau
ggugccguaacuucgggagaaggcacgcugauuagcucgccugaucaguc
gaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaa
acacgaaaguggacguauacggugugacgccugcccggugccggaagguu
aaugggguugcaaagcucucgaagccccgguaaacggcggccguaacuau
aacgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcac
gaauggcguaaugauggccaggcugucuccacccgagacucagugaaauu
gaacucgcugugaagaugcaguguacccgcggcaagacggaaagaccccg
ugaaccuuuacuauagcuugacacugaacauugagccuugauguguagga
uaggugggaggcuuugaaguguggacgccagucugcauggagccggccuu
gaaauaccacccuuuaauguuugauguucuaacccgaauccggggacagu
gucugguggguaguuugacuggggcggucuccuccuaaagaguaacggag
gagcacgaagguuggcuaauccuggcaucaggagguuagugcaauggcau
aagccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcaggu
cauagugauccgguggucugaauggaagggccaucgucaacggaaaaggu
acuccggggauaacaggcugauaccgcccaagaguucauaucgacggcgg
uguuuggcaccucgaugucggcucaucacauccuggggcugaaguagguc
ccaaggguauggcuguucgccauuuaaagugguacgcgagcuggguuuag
aacgucgugagacaguucggucccuaucugccgugggcggagaacugagg
ggggcugcuccuaguacgagaggaccggaguggacgcaucacugguguuc
ggguugucagccauggcacugcccgguagcuaaaugcggagagauaagug
cugaaagcaucuaagcacgaaacuugccccgagaugaguucucccgaagg
aacguugaagacgacgacguugauaggccggguguguaagcgcagcaaug
cguugagcuaaccgguacuaaugaaccgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4w Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements
• Resolution: 15.0 Å
• Binding residue (original residue number in PDB): K5 R52 H55 K95 Y97 Y98
• Binding residue (residue number reindexed from 1): K5 R52 H55 K95 Y97 Y98

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v4w, PDBe:4v4w, PDBj:4v4w
• PDBsum: 4v4w
• PubMed: 16713583
• UniProt: P0A7K6|RL19_ECOLI Large ribosomal subunit protein bL19 (Gene Name=rplS)