Structure of PDB 4wf1 Chain B5 Binding Site BS01

Receptor Information

>4wf1 Chain B5 (length=190) Species: 300852 (Thermus thermophilus HB8)

KVYTIDEAARTAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVR
VLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFVMGAVGSKLGRIL
GPRGLNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPE
KLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVR

Ligand information

>4wf1 Chain BA (length=2897)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauguguaggauaggugggaggcuuugaaguguggacgccagucugcaug
gagccgaccuugaaauaccacccuuuaauguuugauguucuaacguugac
ccguaauccggguugcggacagugucugguggguaguuugacuggggcgg
ucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugguc
ggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgu
gacggcgcgagcaggugcgaaagcaggucauagugauccggugguucuga
auggaagggccaucgcucaacggauaaaagguacuccggggauaacaggc
ugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugu
cggcucaucacauccuggggcugaaguaggucccaaggguauggcuguuc
gccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguuc
ggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagu
acgagaggaccggaguggacgcaucacugguguucggguugucaugccaa
uggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucu
aagcacgaaacuugccccgagaugaguucucccugacccuuuaagggucc
ugaaggaacguugaagacgacgacguugauaggccggguguguaagcgca
gcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wf1 Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.
• Resolution: 3.09 Å
• Binding residue (original residue number in PDB): A36 K37 T41 E43 H45 K47 W108 M109 L137 G170 A171 V176 G177 S212 V215 M219
• Binding residue (residue number reindexed from 1): A12 K13 T17 E19 H21 K23 W84 M85 L105 G136 A137 V142 G143 S178 V181 M185

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0006417 regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4wf1, PDBe:4wf1, PDBj:4wf1
• PDBsum: 4wf1
• PubMed: 25368144
• UniProt: Q5SLP7|RL1_THET8 Large ribosomal subunit protein uL1 (Gene Name=rplA)