Structure of PDB 5tgm Chain Q2 Binding Site BS01

Receptor Information

>5tgm Chain Q2 (length=105) Species: 4932 (Saccharomyces cerevisiae)

VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFG
GQTKPVFHKKAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKG
QALQF

Ligand information

>5tgm Chain 1 (length=3149)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaaugccucgucau
cuaauuagugacgcgcaugaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaagag
acauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucca
cguucuagcauucaaggucccauucggggcugauccggguugaagacauu
gucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgca
gauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaa
ggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaa
aguguggccuaucgauccuuuagucccucggaauuugaggcuagaggugc
cagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucaua
gcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaa
gcagaauucgguaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaaug
uuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucggau
aauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccaucc
gcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcgg
ugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuug
uggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaagg
ccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaau
cauuuguauacgacuuagauguacaacgggguauuguaagcaguagagua
gccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5tgm Molecular insights into protein synthesis with proline residues.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): V2 N3 P5 K9 T10 K13 R18 K19 H20 Y28 A30 K32 A33 S34 F36 Q38 G39 R41 R42 R45 K46 G49 F50 G52 Q53 P56 V57 F58 K60 K61 A62 K63 T65 K67 V69 T79 R80 Q82 K86 R87 C88 K89 K97 K98
• Binding residue (residue number reindexed from 1): V1 N2 P4 K8 T9 K12 R17 K18 H19 Y27 A29 K31 A32 S33 F35 Q37 G38 R40 R41 R44 K45 G48 F49 G51 Q52 P55 V56 F57 K59 K60 A61 K62 T64 K66 V68 T78 R79 Q81 K85 R86 C87 K88 K96 K97

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:5tgm, PDBe:5tgm, PDBj:5tgm
• PDBsum: 5tgm
• PubMed: 27827794
• UniProt: P0CX27|RL44A_YEAST Large ribosomal subunit protein eL42A (Gene Name=RPL42A)