Structure of PDB 5gag Chain O Binding Site BS01

Receptor Information

>5gag Chain O (length=125) Species: 562 (Escherichia coli)

MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEP
LITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKC
GFRAGDNAPMAYIELVDRSEKAEAA

Ligand information

>5gag Chain A (length=2883)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuggcgu
gugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagca
agguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcgu
uaaguugcaggguauagacccgaaacccggugaucuagccaugggcaggu
ugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaaa
auuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggaga
uagcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucu
ccggggguagagcacuguuucggcaagggguuaccaacccgaugcaaacu
gcgaauaccggagaauguuaucacgggagacacacggcgggugcuaacgu
ccgucgugaagagggaaacaacccagaccgccagcuaaggucccaaaguc
augguuaagugggaaacgaugugggaaggcccagacagccaggauguugg
cuuagaagcagccaucauuuaaagaaagcguaauagcucacuggucgagu
cggccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcgg
cagcgacgcugcguuguuggguaggggagcguucuguaagccugcgaagg
ugugcugugaggcaugcuggagguaucagaagugcgaaugcugacauaag
uaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccu
guccaacguuaaucggggcagggugagucgaccccuaaggcgaggccgaa
aggcguagucgaugggaaacagguuaauauuccuguacuugguguuacug
cgaaggggggacggagaaggcuauguuggccgggcgacgguugucccggu
uuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugag
gcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcuucca
ggaaaagccucuaagcaucagguaacaucaaaucguaccccaaaccgaca
cagguggucagguagagaauaccaaggcgcuugagagaacucgggugaag
gaacuaggcaaaauggugccguaacuucgggagaaggcacgcugauaugu
aggugaggucccucgcggauggagcugaaaucagucgaagauaccagcug
gcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaaguggac
guauacggugugacgccugcccggugccggaagguuaauugaugggguua
gcgcaagcgaagcucuugaucgaagccccgguaaacggcggccguauaac
gguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaa
uggcguaaugauggccaggcugucuccacccgagacucagugaaauugaa
cucgcugugaagaugcaguguacccgcggcaagacggaaagaccccguga
accuuuacuauagcuugacacugaacauugagccuugauguguaggauag
gugggaggcuuugaaguguggacgccagucugcauggagccgaccuugaa
auaccacccuuuaauguuugauguucuaacguugacccguaauccggguu
gcggacagugucugguggguaguuugacuggggcggucuccuccuaaaga
guaacggaggagcacgaagguuggcuaauccuggucggacaucaggaggu
uagugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcag
gugcgaaagcaggucauagugauccggugguucugaauggaagggccauc
gcucaacggauaaaagguacuccggggauaacaggcugauaccgcccaag
aguucauaucgacggcgguguuuggcaccucgaugucggcucaucacauc
cuggggcugaaguaggucccaaggguauggcuguucgccauuuaaagugg
uacgcgagcuggguuuagaacgucgugagacaguucggucccuaucugcc
gugggcgcuggagaacugaggggggcugcuccuaguacgagaggaccgga
guggacgcaucacugguguucggguugucaugccaauggcacugcccggu
agcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuug
ccccgagaugaguucucccugacccuuuaaggguccugaaggaacguuga
agacgacgacguugauaggccggguguguaagcgcagcgaugcguugagc
uaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gag Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): M1 R2 H3 R4 K5 S6 R8 Q9 L10 N11 N13 H16 R17 R22 N23 M24 S27 H31 I34 T36 T37 P39 K40 K42 R46 E49 T53 R64 F67 A68 R69 R71 N73 E74 A77 R90 A91 G92 G93 T95 R96 K99 R103 A104 G105 D106 N107 A108
• Binding residue (residue number reindexed from 1): M1 R2 H3 R4 K5 S6 R8 Q9 L10 N11 N13 H16 R17 R22 N23 M24 S27 H31 I34 T36 T37 P39 K40 K42 R46 E49 T53 R64 F67 A68 R69 R71 N73 E74 A77 R90 A91 G92 G93 T95 R96 K99 R103 A104 G105 D106 N107 A108

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:5gag, PDBe:5gag, PDBj:5gag
• PDBsum: 5gag
• PubMed: 26804923
• UniProt: P0AG44|RL17_ECOLI Large ribosomal subunit protein bL17 (Gene Name=rplQ)