Structure of PDB 6mtc Chain B Binding Site BS01

Receptor Information

>6mtc Chain B (length=394) Species: 9986 (Oryctolagus cuniculus)

SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKA
GMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRT
FKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDDAGKRQLDKDFS
SMKKYCQVIRVLAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERL
EQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKV
ACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSL
LVQTKRRALEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Ligand information

>6mtc Chain 5 (length=3597)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugccgccgcgcucuccccccugggggggccgggccaccccucc
cacggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgc
gccgucgggcccggggggccacgcgucccccgcgagcgcacggggucggc
ggcgaugucggcuacccacccgacccgucuugaaacacggaccaaggagu
cuaacacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaa
ggugaaggccggcggcgcgccgccggccgaggugggaucccgaggccuuc
caguccgccgagggcgcaccaccggcccgucucgcccgccgcgccgggga
gguggagcacgagcgcacguguuaggacccgaaagauggugaacuaugcc
ugggcagggcgaagccagaggaaacucugguggagguccguagcgguccu
gacgugcgaaucggucguccgaccuggguauaggggcgaaagacuaaucg
aaccaucuaguagcugguucccuccaaaguuucccucaggauagcuggcg
cucuccgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccg
aaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggcuc
gcugguguggagccgggcguggaaugcgagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
gcaggaugguggccauggaagucggaauccgcuaaggaguguguaacaac
ucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgg
gcccauacccggccgucgcuggcagucggcagagcgagaaagagaguggc
gcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaa
gccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggugg
uaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaagggu
uccaugugaacagcaguugaacaugggucagucgguccugagagaugggc
gagcgccguuccgaagggacgggcgauggccuccguugcccucagccgau
cgaaagggagucggguucagauccccgaauccggaguggcggagaugggc
gccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcg
ggagccccggggagaguucucuuuucuuugugaagggcagggcgcccugg
aauggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguu
ccggcggcguccggugagcucucgcuggcccuugaaaauccgggggagag
gguguaaaucucgcgccgggccguacccauauccgcagcaggucuccaag
gugaacagccucuggcauguuggaacaauguagguaagggaagucggcaa
gccggauccguaacuucgggauaaggauuggcucuaagggcuggcagccg
acuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaa
gcaucgcgaaggcccgcggcggguguugacgcgaugugauuucugcccag
ugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcg
ggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauua
gugacgcgcaugaauggaugaacgagauucccacugucccuaccuacuau
ccagcgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaa
gaagacccuguugagcuugacucuagucuggcacggugaagagacaugag
aaguguagaauaagugggaggccgccggugaaauaccacuacucugaucg
uuuuuucacugacccggugaggcgggggggcgagccgggcucucgcuucu
ggcgccaagcgcccggccggccgggcgcgacccgcuccggggacagugcc
agguggggaguuugacuggggcgguacaccugucaaacgguaacgcaggu
guccuaaggcgagcucagggaggacagaaaccucccguggagcagaaggg
caaaagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagc
ggggccucacgauccuucugaccuuuuggguuuuaagcaggaggugucag
aaaaguuaccacagggauaacuggcuuguggcggccaagcguucauagcg
acgucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagca
gaauucaccaagcguuggauuguucacccacuaauagggaacgugagcug
gguuuagaccgucgugagacagguuaguuuuacccuacugaugauguguu
guugccaugguaauccugcucaguacgagaggaaccgcagguucagacau
uugguguaugugcuuggcugaggagccaauggggcgaagcuaccaucugu
gggauuaugacugaacgccucuaagucagaaucccgcccaggcggaacga
uagcgccggagccucgguuggccucggauagccggucccccgccgggguc
cggugcggagagcccuucgucccgggaaacggggcggccggaaagggggc
cgcccucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaa
accauucguagacgaccugcuucugggucgggguuucguacguagcagag
cagcugcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6mtc Structures of translationally inactive mammalian ribosomes.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): S2 H3 R4 K5 F6 S7 A8 P9 R10 H11 G12 S13 L14 G15 F16 P18 R19 K20 R21 S23 H25 R26 K30 S31 M53 H55 R62 S65 A75 Y92 T95 P96 R97 L99 R100 T101 F102 K103 T104 R116 R117 F118 Y119 K120 N121 H123 S125 K126 K128 F130 T131 K132 Y133 Y156 R161 R174 Q175 K176 K177 E182 T223 K224 G225 K226 G227 Y228 K229 G230 R234 K238 K239 R242 K243 T244 H245 R246 G247 L248 R249 K250 V251 A252 C253 I254 G255 A256 W257 H258 A260 R261 V262 S265 R268 A269 Q271 Y274 H276 R277 T278 I280 N281 K282 L317 G318 V321 H322 G324 K334 G335 C336 V337 T340 K341 K342 R343 R348 L352 R357 S372 K373 F374 G375 H376 K385 M389 L392 K393
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 F5 S6 A7 P8 R9 H10 G11 S12 L13 G14 F15 P17 R18 K19 R20 S22 H24 R25 K29 S30 M52 H54 R61 S64 A74 Y91 T94 P95 R96 L98 R99 T100 F101 K102 T103 R115 R116 F117 Y118 K119 N120 H122 S124 K125 K127 F129 T130 K131 Y132 Y155 R160 R173 Q174 K175 K176 E181 T222 K223 G224 K225 G226 Y227 K228 G229 R233 K237 K238 R241 K242 T243 H244 R245 G246 L247 R248 K249 V250 A251 C252 I253 G254 A255 W256 H257 A259 R260 V261 S264 R267 A268 Q270 Y273 H275 R276 T277 I279 N280 K281 L316 G317 V320 H321 G323 K333 G334 C335 V336 T339 K340 K341 R342 R347 L351 R356 S371 K372 F373 G374 H375 K384 M388 L391 K392

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6mtc, PDBe:6mtc, PDBj:6mtc
• PDBsum: 6mtc
• PubMed: 30355441
• UniProt: G1TL06|RL3_RABIT Large ribosomal subunit protein uL3 (Gene Name=RPL3)