Structure of PDB 5zlu Chain Z Binding Site BS01

Receptor Information

>5zlu Chain Z (length=273) Species: 300852 (Thermus thermophilus HB8)

AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIARR

Ligand information

>5zlu Chain V (length=2875)

aagaugguaagggcccacgguggaugccucggcacccgagccgaugaagg
acguggcuaccugcgauaagccagggggagccgguagcgggcguggaucc
cuggauguccgaaugggggaacccggccggcgggaagccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauagguagggugcccgaguaccccg
ugguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaa
guacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaa
gaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagc
agucacggccccgcaagggguuguggcgugccuauugaagcaugagccgg
cgacucacggucgugggcgagcuuaaccguugagcggaggcguagggaaa
ccgaguccgaacagggcgcaaaguccgcggccguggacccgaaaccgggc
gagcuagcccuggccagggugaagcuggggugagacccaguggaggcccg
aaccggugggggaugcaaaccccucggaugagcuggggcuaggagugaaa
agcuaaccgagcccggagauagcugguucuccccgaaaugacuuuagggu
cagccucaggcgcugacuggggccuguagagcacugauagggcuaggggg
cccaccagccuaccaaacccugucaaacuccgaagggucccagguggagc
cugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaa
ccgagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaug
uggcgccgcgaagacagccaggagguuggcuuagaagcagccauccuuua
aagagugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaug
cggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccagg
cgguaggggagcguucccgaugccgaugaaggccgacccgcgaggcggcu
ggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggguga
gaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcg
uaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggca
gccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucua
ggcuagggggaccggagccaauggacgagcccggccagaagcgcagggug
ggagguaggcaaauccgccucccaacaagcucugcgugguggggaagccc
guacgggugacaaccccccgaagccagggagccaagaaaagccucuaagc
acaaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaa
gagcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguugg
ccccguaacuucgggagaaggggugcucccuggggugaugagccccggga
gccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucug
cgaacucguaagaggagguauagggagcgacgcuugcccggugccggaag
gucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggaccc
ggugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaa
aagaccccguggagcuuuacugcagccugguguuggcucuuggucgcgcc
ugcguaggauaggugggagccugugaacccccgccuccggguggggggga
ggcgccggugaaauaccacccuggcgcggcugggggccuaacccucggau
ggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaa
agguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccg
gagagcgcaaggguagaagggggccugacugcgaggccugcaagccgagc
aggggcgaaagccgggccuagugaaccgguggucccguguggaagggcca
ucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccg
agcguccacagcggcggggagguuuggcaccucgaugucggcucgucgca
uccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagc
ggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccg
ccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccg
gaagggacgcaccucugguuucccagcugucccuccaggggcauaagcug
gguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagc
ccgccccaagaugaggccuccacggcgucaagccggaaggacccgggaag
accacccgguggaugggccggggguguaagcgccgcgaggcguugagccg
accggucccaaucguccgaggucuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5zlu Ribosome protection by antibiotic resistance ATP-binding cassette protein.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): K4 P8 Y9 T10 R14 F15 L33 R43 N45 Q46 I49 T50 R52 R54 G56 H58 K59 R60 Y62 R63 I75 Y84 D85 P86 R88 D99 G100 K154 A156 R157 A158 A159 G160 L177 S179 E181 R183 K202 V205 G207 K208 R211 S212 R213 W214 P219 H220 V221 R222 G223 A225 M226 V229 E237 G238 R239 P241 R242 R244 P246 W250 T254 K255 G256 L257 T259 R260 R262 R263 R274
• Binding residue (residue number reindexed from 1): K3 P7 Y8 T9 R13 F14 L32 R42 N44 Q45 I48 T49 R51 R53 G55 H57 K58 R59 Y61 R62 I74 Y83 D84 P85 R87 D98 G99 K153 A155 R156 A157 A158 G159 L176 S178 E180 R182 K201 V204 G206 K207 R210 S211 R212 W213 P218 H219 V220 R221 G222 A224 M225 V228 E236 G237 R238 P240 R241 R243 P245 W249 T253 K254 G255 L256 T258 R259 R261 R262 R273

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5zlu, PDBe:5zlu, PDBj:5zlu
• PDBsum: 5zlu
• PubMed: 29712846
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)