Structure of PDB 5h4p Chain B Binding Site BS01

Receptor Information

>5h4p Chain B (length=386) Species: 559292 (Saccharomyces cerevisiae S288C)

SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

Ligand information

>5h4p Chain 1 (length=3091)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaaguuaaau
auguaagaaguccuuguuacuuaauugaacguggacauuugaaugaagag
cuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaacc
gaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaag
guguuaguucaucuagacagccggacgguggccauggaagucggaauccg
cuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaug
gauggcgcucaagcguguuaccuauacucuaccgucaggguugauaugau
gcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgua
aggucgggucgaacggccucuagugcagaucuuggugguaguagcaaaua
uucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaaca
gcaguuggacguggguuagucgauccuaagagauggggaagcuccguuuc
aaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagau
uccggaaccuggauauggauucuucacgguaacguaacugaauguggaga
cgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauc
accccggaauugguuuauccggagauggggucuuauggcuggaagaggcc
agcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccaca
ggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucuc
caaggugaacagccucuaguugauagaauaauguagauaagggaagucgg
caaaauagauccguaacuucgggauaaggauuggcucuaagggucgggua
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagaagacccuguugagcuugacucuaguuugacauugugaagaga
ucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguucuag
cauucaaggucccauucggggcugauccggguugaagacauugucaggug
gggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguccu
aaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaa
gcccccuugauuuugauuuucagugugaauacaaaccaugaaaguguggc
cuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaaag
uuaccacagggauaacuggcuuguggcagucaagcguucauagcgacauu
gcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaauu
cgguaagcguuggauuguucacccacuaauagggaacgugagcuggguuu
agaccgucgugagacagguuaguuuuacccuacugaugaauguuaccgca
auaguaauugaacuuaguacgagaggaacaguucauucggauaauugguu
uuugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauu
auggcugaacgccucuaagucagaauccaugcuagaacgcggugauuucu
uugcuccacacaauauagauggauacgaauaaggcguccuuguggcgucg
cugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugggu
gcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuugua
uacgacuuagauguacaacgggguauuguaagcaguagaguagccuuguu
guuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5h4p Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1
• Resolution: 3.07 Å
• Binding residue (original residue number in PDB): S2 H3 R4 K5 E7 R10 H11 H13 L14 G15 F16 P18 R19 K20 R21 I25 R26 R28 K30 A31 M53 T55 R62 S65 A75 Y92 T95 P96 R97 L99 R100 S101 L102 T104 R116 R117 F118 Y119 K120 N121 Y123 K124 S125 K126 K128 A129 F130 K132 Y133 R150 K153 Y154 R159 Q173 K174 K175 L178 E180 T221 K222 G223 H224 G225 F226 G228 H231 R232 K236 K237 R240 K241 T242 H243 R244 G245 R247 K248 A250 C251 A254 W255 H256 P257 A258 H259 V260 W262 S263 R266 A267 G268 Q269 Y272 S274 R275 T276 N279 G309 H313 E316 K325 G326 C327 I328 P329 G330 R332 K333 R339 L342 R348 S363 K364 F365 G366 K367 K376 M380 K384
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 E6 R9 H10 H12 L13 G14 F15 P17 R18 K19 R20 I24 R25 R27 K29 A30 M52 T54 R61 S64 A74 Y91 T94 P95 R96 L98 R99 S100 L101 T103 R115 R116 F117 Y118 K119 N120 Y122 K123 S124 K125 K127 A128 F129 K131 Y132 R149 K152 Y153 R158 Q172 K173 K174 L177 E179 T220 K221 G222 H223 G224 F225 G227 H230 R231 K235 K236 R239 K240 T241 H242 R243 G244 R246 K247 A249 C250 A253 W254 H255 P256 A257 H258 V259 W261 S262 R265 A266 G267 Q268 Y271 S273 R274 T275 N278 G308 H312 E315 K324 G325 C326 I327 P328 G329 R331 K332 R338 L341 R347 S362 K363 F364 G365 K366 K375 M379 K383

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:1990145 maintenance of translational fidelity

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:5h4p, PDBe:5h4p, PDBj:5h4p
• PDBsum: 5h4p
• PubMed: 28112732
• UniProt: P14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)