Structure of PDB 4v7u Chain DS Binding Site BS01

Receptor Information

>4v7u Chain DS (length=110) Species: 83333 (Escherichia coli K-12)

METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKV
LESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRT
SHITVVVSDR

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): I4 K6 H7 R8 H9 S13 Q15 K16 R18 R25 N40 K41 K42 K49 S53 A56 N57 H60 F75 D77 E78 P80 K83 R84 P87 R88 A89 K90 G91 D94 I96 L97 K98
• Binding residue (residue number reindexed from 1): I4 K6 H7 R8 H9 S13 Q15 K16 R18 R25 N40 K41 K42 K49 S53 A56 N57 H60 F75 D77 E78 P80 K83 R84 P87 R88 A89 K90 G91 D94 I96 L97 K98

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042255 ribosome assembly
• GO:0042256 cytosolic ribosome assembly
• GO:0046677 response to antibiotic
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

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

External links

• PDB: RCSB:4v7u, PDBe:4v7u, PDBj:4v7u
• PDBsum: 4v7u
• PubMed: 20876128
• UniProt: P61175|RL22_ECOLI Large ribosomal subunit protein uL22 (Gene Name=rplV)