Structure of PDB 6gxp Chain L Binding Site BS01

Receptor Information

>6gxp Chain L (length=143) Species: 562 (Escherichia coli)

RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFE
GGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANII
GIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE

Ligand information

>6gxp Chain A (length=2896)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaaggggguacuuaccaacccgaug
caaacugcgaauaccggagaauguuaucacgggagacacacggcgggugc
uaacguccgucgugaagagggaaacaacccagaccgccagcuaagguccc
aaagucaugguuaagugggaaacgaugugggaaggcccagacagccagga
uguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacugg
ucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaag
cugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagc
cugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugc
ugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacca
aggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggc
gaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuug
guguuacugcgaaggggggacggagaaggcuauguuggccgggcgacggu
ugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauc
aaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcc
cugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccc
aaaccgacacagguggucagguagagaauaccaaggcgcuugagagaacu
cgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacg
cugauauguaggugaggucccucgcggauggagcugaaaucagucgaaga
uaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacg
aaaguggacguauacggugugacgccugcccggugccgggagguuaauug
augggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaauggcguaaugauggccaggcugucuccacccgagacu
cagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auguguaggauaggugggaggcuuugaaguguggacgccagucugcaugg
agccgaccuugaaauaccacccuuuaauguuugauguucuaacguugacc
cguaauccggguugcggacagugucugguggguaguuugacuggggcggu
cuccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucg
gacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgug
acggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaa
uggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcu
gauaccgcccaagaguucauaucgacggcgguguuuggcaccucgauguc
ggcucaucacauccuggggcugaaguaggucccaaggguauggcuguucg
ccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucg
gucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagua
cgagaggaccggaguggacgcaucacugguguucggguugucaugccaau
ggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucua
agcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccu
gaaggaacguugaagacgacgacguugauaggccggguguguaagcgcag
cgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..].>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>...................<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<<<..>>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<
<<<...<<<<<<......>>>>>>...>.>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
..>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.<<..>>..>>...>>>>.>
>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<..
....>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((
.....<<<<<<...........<<..<<<<<..<<........<<<<<.<
.....<<.........>>.....>........<<<......>>>..>>>>
>....>>..>>>>>.>>...........))).....>>>>>>.>>>...>
>>>>>><<<<<..<......>..>>>>>....>>>>>><.<<<<<...<<
<......<<<<<<<<....>>>>>>>>...>>>..>>>>>..>.....>>
>>>><......<<.....<<<<<<.......>>>>>><<<<....<<<<<
.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<
...<<<....>>>...>>>...>>>..<<<<<........>>>>>))<<<
<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((
...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>
..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>
...>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>..
...<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<
<<<<<<.<<...............<<<<<....<<..>>.....>>>>><
<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>>......
......<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<.
...>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<......
..<<<<<<.<<....>>..>>>>>>........>>>>>>>>..>>>>><<
<<<<.......>>>>>>........<...........<<<<<<.....>>
>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>
>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[
......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<
<...........<<<<<..<<<......<<<<<<<<....>>>>>>>>..
.>>>............>>>>>..>>>>.>>>>>>>>>>>...<<<.<<<<
<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>
><<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<...
....>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<<.
...>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.((..>
>>>..))>>>>>>>.............>>>>..]]>>>>.......<<<<
...<<<<<<...<<.......>>...>>>>>>....>>>.>.......<<
<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>
>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>.
...]]..)))>>>>>>>>....<<<<<<<...<<<<...<<<<<<.....
..........>>>>>>..<<<<<...<<<<...<<<<<<<<<<<))).>>
>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...........
>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>>..
...<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<.
...>>>>>...>>...>>>>>.>>>.....>>.....>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gxp Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1.
• Resolution: 4.4 Å
• Binding residue (original residue number in PDB): L3 N4 P8 G11 S12 K13 K14 G16 K17 R18 L19 G20 R21 G22 G24 S25 K29 T30 G32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 R47 F50 G52 G53 Q54 M55 Y58 R59 R60 L61 P62 K63 F64 G65 F66 S68 R69 K70 E76 R78 N99 I103 K109 I111 L112 R126 T128
• Binding residue (residue number reindexed from 1): L2 N3 P7 G10 S11 K12 K13 G15 K16 R17 L18 G19 R20 G21 G23 S24 K28 T29 G31 R32 G33 H34 K35 G36 Q37 K38 S39 R40 S41 G42 R46 F49 G51 G52 Q53 M54 Y57 R58 R59 L60 P61 K62 F63 G64 F65 S67 R68 K69 E75 R77 N98 I102 K108 I110 L111 R125 T127

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• 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:6gxp, PDBe:6gxp, PDBj:6gxp
• PDBsum: 6gxp
• PubMed: 30076302
• UniProt: P02413|RL15_ECOLI Large ribosomal subunit protein uL15 (Gene Name=rplO)