Structure of PDB 4v56 Chain BV Binding Site BS02

Receptor Information

>4v56 Chain BV (length=94) Species: 562 (Escherichia coli)

MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNM
QAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Ligand information

>4v56 Chain BB (length=2841)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaacaacccgaugcaaacugcgaau
accggagaauguuaucacgggagacacacggcgggugcuaacguccgucg
ugaagagggaaacaacccagaccgccagcuaaggucccaaagucaugguu
aagugggaaacgaugugggaaggcccagacagccaggauguuggcuuaga
agcagccaucauuuaaagaaagcguaauagcucacuggucgagucggccu
gcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcga
cgcuuaugcguuguuggguaggggagcguucuguaagccugcgaaggugu
gcugugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaa
cgauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccuguc
caacguuaaucggggcagggugagucgaccccuaaggcgaggccgaaagg
cguagucgaugggaaacagguuaauauuccuguacuugguguuacugcga
aggggggacggagaaggcuauguuggccgggcgacgguugucccgguuua
agcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcg
ugaugacgaggcacuacggugcugaagcaacaaaugcccugcuuccagga
aaagccucuaagcaucagguaacaucaaaucguaccccaaaccgacacag
guggucagguagagaauaccaaggcgcuugagagaacucgggugaaggaa
cuaggcaaaauggugccguaacuucgggagaaggcacgcugauauguagg
ugaggucccucgcggauggagcugaaaucagucgaagauaccagcuggcu
gcaacuguuuauuaaaaacacagcacugugcaaacacgaaaguggacgua
uacggugugacgccugcccggugccggaagguuaauugaugggguuagcg
caagcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaa
cgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacga
auggcguaaugauggccaggcugucuccacccgagacucagugaaauuga
acucgcugugaagaugcaguguacccgcggcaagacggaaagaccccgug
aaccuuuacuauagcuugacacugaacauugagccuugauggaagugugg
acgccagucugcauggcuuuaauguuugauguucuaacguugacccguaa
uccggguugcggacagugucugguggguaguuugacuggggcggucuccu
ccuaaagaguaacggaggagcacgaagguuggcuaauccuggucggacau
caggagguuagugcaauggcauaagccagcuugacugcgagcgugacggc
gcgagcaggugcgaaagcaggucauagugauccggugguucugaauggaa
gggccaucgcucaacggauaaaagguacuccggggauaacaggcugauac
cgcccaagaguucauaucgacggcgguguuuggcaccucgaugucggcuc
aucacauccuggggcugaaguaggucccaaggguauggcuguucgccauu
uaaagugguacgcgagcuggguuuagaacgucgugagacaguucgguccc
uaucugccgugggcgcuggagaacugaggggggcugcuccuaguacgaga
ggaccggaguggacgcaucacugguguucggguugucaugccaauggcac
ugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcac
gaaacuugccccgagaugaguucucccugacccuuuaaggguccugaagg
aacguugaagacgacgacguugauaggccggguguguaagcgcagcgaug
cguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..].>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.<...<<<...<<<.<<<<.......>>>>.>>>..>>.>...>
.>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>
>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.
..........<<..<<<<<..<<........<<<<<.<<...<<<<....
...>>>>...>>........<<<......>>>..>>>>>....>>..>>>
>>.>>...........))).....>>>>>>.>>>...>>>>>>><<<<<<
<<<....>>>>>>>>>....>>>>>><.<<<<<...<<<......<<<<<
<<<....>>>>>>>>...>>>..>>>>>..>.....>>>>>>.......<
<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<
...<<.....>>.>>>>>>....((<<<.<<<...<<<...<<<....>>
>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<<<..
.<<<<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>><<.
.<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>
>...>><..<<<<<<..>>>>>>...>>>>>>...>>>...>>>>.....
....>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<......>
>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<...
............<<<<<...............>>>>><<<<<<.....<<
<...<<<<.....>>>>...>>>...>>>>>>............<<<<<<
<<<..<<<.........>>>..<<<<<<<.....<<<....>>>......
.>>>>>>>.<<<<<.<<<..<<<<<<<..<<<....<...<<<<<..<<.
...>>...>>>>>..>.....>>>>>>>>..>>>>><<<<<<.......>
>>>>>........<...........<<<<<<.....>>>>>>.....>..
..>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>........
...<<<<<........>>>>>..<<<<<<<<.(((.[[......<<<<.[
[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<<.....<<<<<<
<<....>>>>>>>>....>>>>.>>>>>>>>>>>...<<<.<<<<<<...
..>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<
<<...........>>>>>>.(<<...<<<<<<<...<<<<<<.......>
>>>>>.....<<)..(((>>....>>>>>>>...<<<<..<<<<....>>
>>..>>>>.<<<....>>>.>>))).......<<<<<<<.((..>>>>..
))>>>>>>>.............>>>>..]]>>>>.......<<<<...<<
<<<<...<<.......>>...>>>>>>....>>>.>.......<<<<<.<
<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>.
....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....]]
..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<..........
.....>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>>>>.
.>>>>>...>>>>.>>>>>...<<<....<<<<<...........>>>>>
....>>>.>>>>.......>>>>>>>..<<<<<<...>>>>>>.....<<
..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<....>>
>>>...>>...>>>>>.>>>.....>>.....>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v56 A steric block in translation caused by the antibiotic spectinomycin.
• Resolution: 3.93 Å
• Binding residue (original residue number in PDB): K46 N49 K83 P84 K85
• Binding residue (residue number reindexed from 1): K46 N49 K83 P84 K85

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0009314 response to radiation
• GO:0017148 negative regulation of 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:4v56, PDBe:4v56, PDBj:4v56
• PDBsum: 4v56
• PubMed: 17696316
• UniProt: P68919|RL25_ECOLI Large ribosomal subunit protein bL25 (Gene Name=rplY)