Structure of PDB 4v7u Chain D1 Binding Site BS01

Receptor Information

>4v7u Chain D1 (length=50) Species: 83333 (Escherichia coli K-12)

GIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAK

Ligand information

>4v7u Chain DA (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: 4v7u Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): G3 R5 K7 F19 Y20 T22 T23 K29 L33 L35 K36 F38 Q44 H45
• Binding residue (residue number reindexed from 1): G1 R3 K5 F17 Y18 T20 T21 K27 L31 L33 K34 F36 Q42 H43

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

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:4v7u, PDBe:4v7u, PDBj:4v7u
• PDBsum: 4v7u
• PubMed: 20876128
• UniProt: P0A7N9|RL33_ECOLI Large ribosomal subunit protein bL33 (Gene Name=rpmG)