Structure of PDB 4v6s Chain AP Binding Site BS01

Receptor Information

>4v6s Chain AP (length=127) Species: 562 (Escherichia coli)

MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEP
LITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKC
GFRAGDNAPMAYIELVDRSEKAEAAAE

Ligand information

>4v6s Chain AB (length=2904)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugauguguaggauaggugggaggcuuugaaguguggacgccaguc
ugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6s Structural characterization of mRNA-tRNA translocation intermediates.
• Resolution: 13.1 Å
• Binding residue (original residue number in PDB): M1 R2 H3 R4 K5 S6 G7 R8 Q9 L10 N11 R12 N13 S14 S15 H16 R17 R22 N23 R30 H31 K35 T37 L38 P39 K40 K42 E43 R45 R46 E49 T53 V60 A61 N62 R63 R64 A68 R69 R71 D72 R90 G92 G93 Y94 R96 L98 K99 F102 R103 G105 D106 N107
• Binding residue (residue number reindexed from 1): M1 R2 H3 R4 K5 S6 G7 R8 Q9 L10 N11 R12 N13 S14 S15 H16 R17 R22 N23 R30 H31 K35 T37 L38 P39 K40 K42 E43 R45 R46 E49 T53 V60 A61 N62 R63 R64 A68 R69 R71 D72 R90 G92 G93 Y94 R96 L98 K99 F102 R103 G105 D106 N107

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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:4v6s, PDBe:4v6s, PDBj:4v6s
• PDBsum: 4v6s
• PubMed: 22467828
• UniProt: P0AG44|RL17_ECOLI Large ribosomal subunit protein bL17 (Gene Name=rplQ)