Structure of PDB 4v9d Chain DW Binding Site BS01

Receptor Information
>4v9d Chain DW (length=75) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLF
AKADGKVKFEVKGPKNRKFISIEAE
Ligand information
>4v9d Chain DA (length=2896) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggagguuaauug
augggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaauggcguaaugauggccaggcugucuccacccgagacu
cagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auguguaggauaggugggaggcuuugaaguguggacgccagucugcaugg
agccgaccuugaaauaccacccuuuaauguuugauguucuaacguugacc
cguaauccggguugcggacagugucugguggguaguuugacuggggcggu
cuccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucg
gacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgug
acggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaa
uggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcu
gauaccgcccaagaguucauaucgacggcgguguuuggcaccucgauguc
ggcucaucacauccuggggcugaaguaggucccaaggguauggcuguucg
ccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucg
gucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagua
cgagaggaccggaguggacgcaucacugguguucggguugucaugccaau
ggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucua
agcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccu
gaaggaacguugaagacgacgacguugauaggccggguguguaagcgcag
cgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu
<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<............>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<<<<<.>>>>.>>...>>>>.
>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<.
.....>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<((
(.....<<<<<<...........<<..<<<<<..<<........<<<<<.
<<<..<.............>..>>>........<<<......>>>..>>>
>>....>>..>>>>>.>>...........))).....>>>>>>.>>>...
>>>>>>><<<<<<.<......>.>>>>>>....>>>>>><.<<<<<...<
<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>..>.....>
>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<<<
<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<
<...<<<....>>>...>>>...>>>..<<<<<........>>>>>))<<
<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....((
(...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>
>..>>>>...>>>>...>>...<<<<<....>>>>>....>>>>>...>>
>...>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>.
....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<
<<<<<<<.<<...............<<<<<...............>>>>>
<<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>>.....
.......<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<
....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<.<<<......
..<<<<<..<<....>>...>>>>>........>>>>>>>>..>>>>><<
<<<<.......>>>>>>........<...........<<<<<<.....>>
>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>
>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[
......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<
<...........<<<<<..<<<......<<<<<<<<....>>>>>>>>..
.>>>............>>>>>..>>>>.>>>>>>>>>>>...<<<.<<<<
<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>
><<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<...
....>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<<.
...>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.((..>
>>>..))>>>>>>>.............>>>>..]]>>>>.......<<<<
...<<<<<<...<<.......>>...>>>>>>....>>>.>.......<<
<<<..<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>
>>>>.....>>>>>......>>>.>>....<<<<<<<....>>>.>>>>.
...]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.....
..........>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>
>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...........
>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>>..
...<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<.
...>>>>>...>>...>>>>>.>>>.....>>.....>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v9d Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
N8 R10 D11 S12 E13 A14 K15 R16 K20 F22 G23 E25 L28 A29 G30 S31 I32 R35 R37 G38 T39 K40 F41 G50 R51 D52 H53 F56 F65 K71 R73 K74
Binding residue
(residue number reindexed from 1)
N2 R4 D5 S6 E7 A8 K9 R10 K14 F16 G17 E19 L22 A23 G24 S25 I26 R29 R31 G32 T33 K34 F35 G44 R45 D46 H47 F50 F59 K65 R67 K68
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4v9d, PDBe:4v9d, PDBj:4v9d
PDBsum4v9d
PubMed21596992
UniProtP0A7L8|RL27_ECOLI Large ribosomal subunit protein bL27 (Gene Name=rpmA)

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