Structure of PDB 5gah Chain Y Binding Site BS01

Receptor Information

>5gah Chain Y (length=77) Species: 562 (Escherichia coli)

SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRV
SAKGMRVIDKKGIDTVLAELRARGEKY

Ligand information

>5gah 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: 5gah 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): S2 R3 K10 R11 G15 N16 N17 R18 S19 A21 L22 N23 K26 R27 R28 F29 L30 P31 N32 H34 H36 R37 R50 A53 K54 M56 R57 K61 K62
• Binding residue (residue number reindexed from 1): S1 R2 K9 R10 G14 N15 N16 R17 S18 A20 L21 N22 K25 R26 R27 F28 L29 P30 N31 H33 H35 R36 R49 A52 K53 M55 R56 K60 K61

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• 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:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5gah, PDBe:5gah, PDBj:5gah
• PDBsum: 5gah
• PubMed: 26804923
• UniProt: P0A7M2|RL28_ECOLI Large ribosomal subunit protein bL28 (Gene Name=rpmB)