Structure of PDB 5dgf Chain q2 Binding Site BS01

Receptor Information

>5dgf Chain q2 (length=105) Species: 559292 (Saccharomyces cerevisiae S288C)

VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFG
GQTKPVFHKKAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKG
QALQF

Ligand information

>5dgf Chain 5 (length=3169)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgaaaugaccuugaccuauucucaaac
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuagacagccggacgguggccauggaagucg
gaauccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccu
gaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguug
auaugaugcccugacgaguaggcaggcguggaggucagugacgaagccua
gaccguaaggucgggucgaacggccucuagugcagaucuuggugguagua
gcaaauauucaaaugagaacuuugaagacugaaguggggaaagguuccac
gucaacagcaguuggacguggguuagucgauccuaagagauggggaagcu
ccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgg
uuaagauuccggaaccuggauauggauucuucacgguaacguaacugaau
guggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaaca
gcuuaucaccccggaauugguuuauccggagauggggucuuauggcugga
agaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaa
auccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagc
aggucuccaaggugaacagccucuaguugauagaauaauguagauaaggg
aagucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggg
ucggacgaucaacuuagaacugguacggacaaggggaaucugacugucua
auuaaaacauagcauugcgauggucagaaagugauguugacgcaauguga
uuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcg
gguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucg
ucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
agagacauagagggcuaccuuuauaguuucuuuacuuauucaaugaagcg
gagcuggaauucauuuuccacguucuagcauucaaggucccauucggggc
ugauccggguugaagacauugucagguggggaguuuggcuggggcggcac
aucuguuaaacgauaacgcagauguccuaaggggggcucauggagaacag
aaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuuca
gugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucg
gaauuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuu
guggcagucaagcguucauagcgacauugcuuuuugauucuucgaugucg
gcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguucac
ccacuaauagggaacgugagcuggguuuagaccgucgugagacagguuag
uuuuacccuacugaugaauguuaccgcaauaguaauugaacuuaguacga
gaggaacaguucauucggauaauugguuuuugcggcugucugaucaggca
uugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaaguca
gaauccaugcuagaacgcggugauuucuuugcuccacacaauauagaugg
auacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaa
cggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaaugu
cauuuugcguggggauaaaucauuuguauacgacuuagauguacaacggg
guauuguaagcaguagaguagccuuguuguuacgaucugcugagauuaag
ccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dgf Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): V2 N3 P5 R8 T10 Y11 K13 K15 K19 H20 Y28 A30 G31 A33 S34 F36 A37 Q38 G39 R41 R45 K46 G49 F50 G52 Q53 T54 K55 P56 V57 F58 K60 K61 A62 K63 T65 K66 K67 V69 R80 Q82 T84 K86 R87 C88 K89 K97 K98 K100
• Binding residue (residue number reindexed from 1): V1 N2 P4 R7 T9 Y10 K12 K14 K18 H19 Y27 A29 G30 A32 S33 F35 A36 Q37 G38 R40 R44 K45 G48 F49 G51 Q52 T53 K54 P55 V56 F57 K59 K60 A61 K62 T64 K65 K66 V68 R79 Q81 T83 K85 R86 C87 K88 K96 K97 K99

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