Structure of PDB 6r6g Chain C Binding Site BS01

Receptor Information

>6r6g Chain C (length=362) Species: 9986 (Oryctolagus cuniculus)

ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQP
YAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRM
FAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELP
LVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRR
IQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCI
WTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRV
ERAAAALAAKSD

Ligand information

>6r6g Chain 5 (length=3543)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugcgccgcgcucuccccccucgggggggccgggccaccccucc
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
gaagacccuguugagcuugacucuagucuggcacggugaagagacguuuu
uucacugacccggugaggcgggggggcgagccgggcucucgcuucuggcg
ccaagcgcccggccggccgggcgcgacccgcuccggggacagugccaggu
ggggaguuugacuggggcgguacaccugucaaacgguaacgcaggugucc
uaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaa
agcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcgggg
ccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaa
guuaccacagggauaacuggcuuguggcggccaagcguucauagcgacgu
cgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaau
ucaccaagcguuggauuguucacccacuaauagggaacgugagcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugauguguuguug
ccaugguaauccugcucaguacgagaggaaccgcagguucagacauuugg
uguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggga
uuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauagc
gccggagccucgguuggccucggauagccggucccccgccgggguccggu
gcggagagcccuucgucccgggaaacggggcggccggaaagggggccgcc
cucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacca
uucguagacgaccugcuucugggucgggguuucguacguagcagagcagc
ugcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6r6g Structural and mutational analysis of the ribosome-arresting human XBP1u.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): A2 C3 A4 R5 K29 I36 N38 F39 R45 K46 N47 N48 R49 Q50 Y52 V54 S55 A58 G59 H60 Q61 T62 S63 S66 T69 G70 A72 V73 A74 R75 P77 V79 R80 G83 T84 H85 R86 Q89 N94 M95 C96 R97 G98 R100 M101 F102 A103 P104 K106 R109 R110 R113 R114 N116 T117 T118 Q119 K120 R121 K140 K163 T164 K172 K181 K182 Y184 R188 M189 R190 A191 G192 K193 K195 M196 R197 N198 R199 R204 R205 K219 R222 N223 P225 T233 P242 G243 H245 W267 R268 K274 S275 M281 H282 R291 L293 R303 A304 P305 K307 K308 H310 R311 R312 V313 K316 N321 L322 R323 K327 K333 M335 R336 Q343 N346 R350
• Binding residue (residue number reindexed from 1): A1 C2 A3 R4 K28 I35 N37 F38 R44 K45 N46 N47 R48 Q49 Y51 V53 S54 A57 G58 H59 Q60 T61 S62 S65 T68 G69 A71 V72 A73 R74 P76 V78 R79 G82 T83 H84 R85 Q88 N93 M94 C95 R96 G97 R99 M100 F101 A102 P103 K105 R108 R109 R112 R113 N115 T116 T117 Q118 K119 R120 K139 K162 T163 K171 K180 K181 Y183 R187 M188 R189 A190 G191 K192 K194 M195 R196 N197 R198 R203 R204 K218 R221 N222 P224 T232 P241 G242 H244 W266 R267 K273 S274 M280 H281 R290 L292 R302 A303 P304 K306 K307 H309 R310 R311 V312 K315 N320 L321 R322 K326 K332 M334 R335 Q342 N345 R349

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:6r6g, PDBe:6r6g, PDBj:6r6g
• PDBsum: 6r6g
• PubMed: 31246176
• UniProt: G1SVW5|RL4_RABIT Large ribosomal subunit protein uL4 (Gene Name=RPL4)