Structure of PDB 4v7u Chain D4 Binding Site BS01

Receptor Information

>4v7u Chain D4 (length=38) Species: 83333 (Escherichia coli K-12)

MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

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): M1 R4 A5 S6 V7 K8 K15 I16 K18 R19 D20 I23 R24 P31 K32 K34 R36 Q37 G38
• Binding residue (residue number reindexed from 1): M1 R4 A5 S6 V7 K8 K15 I16 K18 R19 D20 I23 R24 P31 K32 K34 R36 Q37 G38

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• 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: P0A7Q6|RL36_ECOLI Large ribosomal subunit protein bL36A (Gene Name=rpmJ)