Structure of PDB 3j5l Chain D Binding Site BS01

Receptor Information

>3j5l Chain D (length=209) Species: 83333 (Escherichia coli K-12)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

Ligand information

>3j5l Chain A (length=2853)

gguuaacgacuaagcguacacgguggaugcccuggcagucagaggcgaug
aaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguua
uaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuauc
auuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacauc
uaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcga
gcgaacggggagcagcccagagccugaaucaguguguguguuaguggaag
cgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaugc
acaugcugugagcucgaugaguagggcgggacacgugguauccugucuga
auauggggggaccauccuccaaggcuaaauacuccugacugaccgauagu
gaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggaguga
aaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggcg
ugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagc
aagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcg
uuaaguugcaggguauagacccgaaacccggugaucuagccaugggcagg
uugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaa
aauuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggag
auagcugguucuccccgaaagcuauuuagguagcgccucgugaauucauc
uccggggguagagcacuguuucggcaagggggucacuuaccaacccgaug
caaacugcgaauaccggagaauguuaucacgggagacacacggcgggugc
uaacguccgucgugaagagggaaacaacccagaccgccagcuaagguccc
aaagucaugguuaagugggaaacgaugugggaaggcccagacagccagga
uguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacugg
ucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaag
cugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagc
cugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugc
ugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacca
aggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggc
gaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuug
guguuacugcgaaggggggacggagaaggcuauguuggccgggcgacggu
ugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauc
aaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcc
cugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccc
aaaccgacacagguggucagguagagaauaccaaggcgcuugagagaacu
cgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacg
cugauauguaggugaggucccucgcggauggagcugaaaucagucgaaga
uaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacg
aaaguggacguauacggugugacgccugcccggugccggaagguuaauug
augggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaauggcguaaugauggccaggcugucuccacccgagacu
cagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auggaaguguggacgccagucugcauggcuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j5l Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.
• Resolution: 6.6 Å
• Binding residue (original residue number in PDB): K8 M11 R13 P23 Q36 N42 Y45 K56 R59 T61 K62 P63 G66 H67 K70 E81 R83 S113 K114 G115 K116 G117 F118 A119 G120 K123 R124 N126 F127 R128 T129 Q130 A132 T133 H134 G135 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 G153 K154 V155 F156 K157 K159 M161 A162 Q164 N167 R169 T171 Q173 S174 L175 G191 V193 P194 A196 T197 K208
• Binding residue (residue number reindexed from 1): K8 M11 R13 P23 Q36 N42 Y45 K56 R59 T61 K62 P63 G66 H67 K70 E81 R83 S113 K114 G115 K116 G117 F118 A119 G120 K123 R124 N126 F127 R128 T129 Q130 A132 T133 H134 G135 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 G153 K154 V155 F156 K157 K159 M161 A162 Q164 N167 R169 T171 Q173 S174 L175 G191 V193 P194 A196 T197 K208

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:3j5l, PDBe:3j5l, PDBj:3j5l
• PDBsum: 3j5l
• PubMed: 24662426
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)