Structure of PDB 5gaf Chain a Binding Site BS01

Receptor Information

>5gaf Chain a (length=58) Species: 562 (Escherichia coli)

AKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAV
SFMVKVEE

Ligand information

>5gaf 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: 5gaf Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon
• Resolution: 4.3 Å
• Binding residue (original residue number in PDB): S12 I14 G15 L17 P18 K19 A22 T23 G26 G28 R30 I32 R38 E39 A43 M47
• Binding residue (residue number reindexed from 1): S11 I13 G14 L16 P17 K18 A21 T22 G25 G27 R29 I31 R37 E38 A42 M46

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5gaf, PDBe:5gaf, PDBj:5gaf
• PDBsum: 5gaf
• PubMed: 26804923
• UniProt: P0AG51|RL30_ECOLI Large ribosomal subunit protein uL30 (Gene Name=rpmD)