Structure of PDB 5l3p Chain 2 Binding Site BS01

Receptor Information

>5l3p Chain 2 (length=63) Species: 83333 (Escherichia coli K-12)

MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDV
ARVKTLLNEKAGA

Ligand information

>5l3p Chain A (length=2890)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacgacuuaccaaccc
gaugcaaacugcgaauaccggagaauguuaucacgggagacacacggcgg
gugcuaacguccgucgugaagagggaaacaacccagaccgccagcuaagg
ucccaaagucaugguuaagugggaaacgaugugggaaggcccagacagcc
aggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagcuca
cuggucgagucggccugcgcggaagauguaacggggcuaaaccaugcacc
gaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguucugu
aagccugcgaaggugugcugugaggcaugcuggagguaucagaagugcga
augcugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaag
accaaggguuccuguccaacguuaaucggggcagggugagucgaccccua
aggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccugua
cuugguguuacugcgaaggggggacggagaaggcuauguuggccgggcga
cgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaa
aaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaa
ugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucgua
ccccaaaccgacacagguggucagguagagaauaccaaggcgcuugagag
aacucgggugaaggaacuaggcaaaauggugccguaacuucgggagaagg
cacgcugauauguaggugaggucccucgcggauggagcugaaaucagucg
aagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaa
cacgaaaguggacguauacggugugacgccugcccggugccgggagguua
auugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacg
gcggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaa
guuccgaccugcacgaauggcguaaugauggccaggcugucuccacccga
gacucagugaaauugaacucgcugugaagaugcaguguacccgcggcaag
acggaaagaccccgugaaccuuuacuauagcuugacacugaacauugagc
cuugauguguaggauaggugggaggcuuugaaguguggacgccagugcga
ccuugaaauaccacccuuuaauguuugauguucuaacguugacccguaau
ccggguugcggacagugucugguggguaguuugacuggggcggucuccuc
cuaaagaguaacggaggagcacgaagguuggcuaauccuggucggacauc
aggagguuagugcaauggcauaagccagcuugacugcgagcgugacggcg
cgagcaggugcgaaagcaggucauagugauccggugguucugaauggaag
ggccaucgcucaacggauaaaagguacuccggggauaacaggcugauacc
gcccaagaguucauaucgacggcgguguuuggcaccucgaugucggcuca
ucacauccuggggcugaaguaggucccaaggguauggcuguucgccauuu
aaagugguacgcgagcuggguuuagaacgucgugagacaguucggucccu
aucugccgugggcgcuggagaacugaggggggcugcuccuaguacgagag
gaccggaguggacgcaucacugguguucggguugucaugccaauggcacu
gcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcacg
aaacuugccccgagaugaguucucccugacccuuuaaggguccugaagga
acguugaagacgacgacguugauaggccggguguguaagcgcagcgaugc
guugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l3p The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): K2 H41 K44 R47 R48 A51 R52 K54 T55 N58
• Binding residue (residue number reindexed from 1): K2 H41 K44 R47 R48 A51 R52 K54 T55 N58

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:5l3p, PDBe:5l3p, PDBj:5l3p
• PDBsum: 5l3p
• PubMed: 27226493
• UniProt: P0A7M6|RL29_ECOLI Large ribosomal subunit protein uL29 (Gene Name=rpmC)