Structure of PDB 5h4p Chain o Binding Site BS01

Receptor Information

>5h4p Chain o (length=95) Species: 559292 (Saccharomyces cerevisiae S288C)

VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFG
GQTKPVFHKKAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGE

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): V2 N3 P5 R8 K9 T10 Y11 K13 K15 R18 K19 H20 Y28 A30 K32 A33 S34 F36 A37 Q38 G39 R41 R42 R45 K46 G49 F50 G52 Q53 T54 K55 P56 V57 F58 K60 K61 A62 K63 K66 K67 R80 Q82 K86 C88
• Binding residue (residue number reindexed from 1): V1 N2 P4 R7 K8 T9 Y10 K12 K14 R17 K18 H19 Y27 A29 K31 A32 S33 F35 A36 Q37 G38 R40 R41 R44 K45 G48 F49 G51 Q52 T53 K54 P55 V56 F57 K59 K60 A61 K62 K65 K66 R79 Q81 K85 C87

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic
• GO:0046898 response to cycloheximide

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5h4p, PDBe:5h4p, PDBj:5h4p
• PDBsum: 5h4p
• PubMed: 28112732
• UniProt: P0CX27|RL44A_YEAST Large ribosomal subunit protein eL42A (Gene Name=RPL42A)