Structure of PDB 3j8g Chain E Binding Site BS01

Receptor Information

>3j8g Chain E (length=201) Species: 83333 (Escherichia coli K-12)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

Ligand information

>3j8g Chain B (length=2874)

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
uuaauaucgaagccccgguaaacggcggccguaacuauaacgguccuaag
guagcgaaauuccuugucggguaaguuccgaccugcacgaauggcguaau
gauggccaggcugucuccacccgagacucagugaaauugaacucgcugug
aagaugcaguguacccgcggcaagacggaaagaccccgugaaccuuuacu
auagcuugacacugaacauugagccuugauguguaggauaggugggaggc
uuugaaguguggacgccagucugcauggagccgaccuugaaauaccaccc
uuuaauguuugauguucuaacguugacccguaauccggguugcggacagu
gucugguggguaguuugacuggggcggucuccuccuaaagaguaacggag
gagcacgaagguuggcuaauccuggucggacaucaggagguuagugcaau
ggcauaagccagcuugacugcgagcgugacggcgcgagcaggugcgaaag
caggucauagugauccggugguucugaauggaagggccaucgcucaacgg
auaaaagguacuccggggauaacaggcugauaccgcccaagaguucauau
cgacggcgguguuuggcaccucgaugucggcucaucacauccuggggcug
aaguaggucccaaggguauggcuguucgccauuuaaagugguacgcgagc
uggguuuagaacgucgugagacaguucggucccuaucugccgugggcgcu
ggagaacugaggggggcugcuccuaguacgagaggaccggaguggacgca
ucacugguguucggguugucaugccaauggcacugcccgguagcuaaaug
cggaagagauaagugcugaaagcaucuaagcacgaaacuugccccgagau
gaguucucccugacccuuuaaggguccugaaggaacguugaagacgacga
cguugauaggccggguguguaagcgcagcgaugcguugagcuaaccggua
cuaaugaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..].>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<........>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<.<.<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
..>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.<<<<.....>>>>..>>..
.>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<..<<<<<..<<........
<<<<<.<<...<<<<.......>>>>...>>........<<<......>>
>..>>>>>....>>..>>>>>.>>...........))).....>>>>>>.
>>>...>>>>>>><<<<<<<<<....>>>>>>>>>....>>>>>><<<<<
<<...<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.>>
.....>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<..
..<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<
<...<<<...<<<....>>>...>>>...>>>..<<<<<........>>>
>>))<<<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<
....(((...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>
>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>
>...>>>...>>>>.........>>>>...>>....>>>>>>>>>>>.>>
>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<
<....<<<<<<<<.<<...............<<<<<....<....>....
.>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>
>............<<<<<<<<<..<<...........>>..<<<<<<<..
...<<<....>>>.......>>>>>>>.<<<<<......<<<<<<...<<
<<........>>>>.>>>>..>>....<<<<<.......>>>>>......
...............<<<<<.......>>>>>..........>>>>>..>
>.>>>>>>>.....>>.>>>>>>>>.>>>>>>...>.>.....<<<<<..
......>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<<<..<<<
<..<<<.<<<<<.<<<<<<<<.<<.<.<......................
..................................................
.>..>.>>.>>>>>>>>...<<<.<<<<<<.....>>>>>>>>>....>>
>>>.>>>...>>>>..<<<<.....>>>><<<<<<...........>>>>
>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<...((
(>>....>>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<....>
>>.>>))).......<<<<<<<.((..>>>>..))>>>>>>>........
.....>>>>..]]>>>>.......<<<<...<<<<<<...<<.......>
>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<<<<<<.
.....>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>
>.>>....<<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....
<<<<<<<<..<<<<..<<<<<<<.....<....>....>>>>>>>.<<<<
<...<<<<...<<<<<<<<<<<))).>>>>>>..>>>>>...>>>>.>>>
>>...<<<....<<<<<...........>>>>>....>>>.>>>>>....
..>>>>>>>..<<<<<<...>>>>>>.....<<..<<<<.........>>
>>....<<<<<<<<..<<....<<<<<....>>>>>...>>...>>>>>.
>>>.....>>.....>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j8g Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly
• Resolution: 5.0 Å
• Binding residue (original residue number in PDB): R21 H29 Q30 Y35 A36 R40 Q41 T43 R44 Q46 K47 T48 R49 A50 G54 S55 K57 K58 W60 Q62 K63 G64 T65 G66 R67 A68 R69 S70 P76 W78 R79 S80 G81 T84 F85 R88 Q94 K95 V96 N97 K98 K99 M100 R102 P129 K130 T131 K132 R162 N163 H165
• Binding residue (residue number reindexed from 1): R21 H29 Q30 Y35 A36 R40 Q41 T43 R44 Q46 K47 T48 R49 A50 G54 S55 K57 K58 W60 Q62 K63 G64 T65 G66 R67 A68 R69 S70 P76 W78 R79 S80 G81 T84 F85 R88 Q94 K95 V96 N97 K98 K99 M100 R102 P129 K130 T131 K132 R162 N163 H165

Gene Ontology

Molecular Function

• GO:0001070 RNA-binding transcription regulator activity
• GO:0003677 DNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0030371 translation repressor activity
• GO:0048027 mRNA 5'-UTR binding
• GO:0060698 endoribonuclease inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006353 DNA-templated transcription termination
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0031555 transcriptional attenuation
• GO:0042255 ribosome assembly
• GO:0045892 negative regulation of DNA-templated transcription
• GO:0046677 response to antibiotic
• GO:2000766 negative regulation of cytoplasmic translation

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:3j8g, PDBe:3j8g, PDBj:3j8g
• PDBsum: 3j8g
• PubMed: 25389271
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)