Structure of PDB 6om0 Chain B Binding Site BS01

Receptor Information

>6om0 Chain B (length=397) Species: 9606 (Homo sapiens)

SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKA
GMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRT
FKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFS
SMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERL
EQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKV
ACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSL
LVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIA

Ligand information

>6om0 Chain t (length=3607)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgcccccggggucggcgggggaccgucccccggaccggcg
accggccgccgccgggcgcauuuccaggcggugcgccgcgaccggcuccg
ggacggcugggaaggcccggcggggaagguggcucggggcccccgagugu
uacagcccccccggcagcagcacucgccgaaucccggggccgagggagcg
agacccgucgccgcgcucuccccccugggggggccgggccaccccuccca
cggcgcgaccgcucucccagggggcggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaa
gggggggacggcggagagcgcacggggucggcggcgacgucggcuaccca
cccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgaguc
gggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcgc
gcucgccggccgaggugggaucccgaggccucuccaguccgccgaggggc
accaccggcccgucucgcccgccgcgccggggagguggagcacgagcgca
cguguuaggacccgaaagauggugaacuaugccugggcagggcgaagcca
gaggaaacucugguggagguccguagcgguccugacgugcaaaucggucg
uccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugg
uucccuccgaaguuucccucaggauagcuggcgcucucgcccacgcaguu
uuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaa
ccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcguggag
ccgggguggaaugcgagugccuagugggccacuuuugguaagcagaacug
gcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcu
caucagaccccagaaaagguguugguugauauagacagcaggacgguggc
cauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaau
caacuagcccugaaaauggauggcgcuggagcgucgggcccauacccggc
cgucgccggcgucgagaguggacgggagcggcggcccggagccccgcgga
cgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagccua
gggcgcgggcccggguggagccgccgcaggugcagaucuuggugguagua
gcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguuccau
gugaacagcaguugaacaugggucagucgguccugagagaugggcgagcg
ccguuccgaagggacgggcgauggccuccguugcccucggccgaucgaaa
gggagucggguucagauccccgaauccggaguggcggagaugggcgccgc
gaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggagc
cccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaugg
guucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggc
ggcguccggugagcucucgcuggcccuugaaaauccgggggagagggugu
aaaucucgcgccgggccguacccauauccgcagcaggucuccaaggugaa
cagccucuggcauguuggaacaauguagguaagggaagucggcaagccgg
auccguaacuucgggauaaggauuggcucuaagggcuggcagccgacuua
gaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcauc
gcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcuc
ugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggagu
aacuaugacucucuuaagguagccaaaugccucgucaucuaauuagugac
gcgcaugaauggaugaacgagauucccacugucccuaccuacuauccagc
gaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaaga
cccuguugagcuugacucuagucuggcacggugaagagacguuuuuucac
ugacccggugaggcgggggggcgagcccgaggggcucucgcuucuggcgc
caagcgcccgcccggccgggcgcgacccgcuccggggacagugccaggug
gggaguuugacuggggcgguacaccugucaaacgguaacgcagguguccu
aaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaaa
gcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggc
cucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaag
uuaccacagggauaacuggcuuguggcggccaagcguucauagcgacguc
gcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaauu
cgccaagcguuggauuguucacccacuaauagggaacgugagcuggguuu
agaccgucgugagacagguuaguuuuacccuacugaugauguguuguugc
caugguaauccugcucaguacgagaggaaccgcagguucagacauuuggu
guaugugcuuggcugaggagccaauggggcgaagcuaccaucugugggau
uaugacugaacgccucuaagucagaaucccgcccaggcggaacgauacgg
cagcgccgcggagccucgguuggccucggauagccgguccccgccggggg
uccggugcggagugcccuucguccugggaaacggggcgcggccggaaagg
cggccgcccccucgcccgucacgcaccgcacguucguggggaaccuggcg
cuaaaccauucguagacgaccugcuucugggucgggguuucguacguagc
agagcagcucccucgcugcgaucuauugaaagucagcccucgacacaagg
guuuguc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6om0 Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): S2 H3 R4 K5 F6 S7 P9 R10 H11 G12 S13 L14 G15 F16 P18 R19 K20 R21 H25 K28 K30 S31 M53 T54 H55 S65 A75 Y92 T95 P96 R97 L99 R100 T101 F102 K103 T104 R117 Y119 K120 N121 H123 K124 S125 K126 K128 F130 K132 Y133 Y156 R174 Q175 K176 L180 E182 T223 K224 G225 K226 G227 Y228 G230 R234 K238 K239 R242 K243 T244 H245 R246 G247 L248 R249 A252 C253 I254 G255 A256 W257 H258 P259 A260 R261 V262 F264 S265 R268 A269 Q271 Y274 H276 R277 T278 E279 I280 K282 L317 G318 H322 G324 K334 C336 V337 T340 K342 R343 R357 S372 K373 F374 G375 H376 M389 K393
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 F5 S6 P8 R9 H10 G11 S12 L13 G14 F15 P17 R18 K19 R20 H24 K27 K29 S30 M52 T53 H54 S64 A74 Y91 T94 P95 R96 L98 R99 T100 F101 K102 T103 R116 Y118 K119 N120 H122 K123 S124 K125 K127 F129 K131 Y132 Y155 R173 Q174 K175 L179 E181 T222 K223 G224 K225 G226 Y227 G229 R233 K237 K238 R241 K242 T243 H244 R245 G246 L247 R248 A251 C252 I253 G254 A255 W256 H257 P258 A259 R260 V261 F263 S264 R267 A268 Q270 Y273 H275 R276 T277 E278 I279 K281 L316 G317 H321 G323 K333 C335 V336 T339 K341 R342 R356 S371 K372 F373 G374 H375 M388 K392

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0071353 cellular response to interleukin-4

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6om0, PDBe:6om0, PDBj:6om0
• PDBsum: 6om0
• PubMed: 31160784
• UniProt: P39023|RL3_HUMAN Large ribosomal subunit protein uL3 (Gene Name=RPL3)