Structure of PDB 5xym Chain C Binding Site BS01

Receptor Information

>5xym Chain C (length=273) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

GIRKYKPTTPGRRGASVSDFAEITRSTPEKSLVRPLHGKGGRNAHGRITT
RHKGGGHKRAYRVIDFRRHDKDGVNAKVAHIEYDPNRTANIALLHYLDGE
KRYIIAPQGLKQGDVIESGANADIKPGNNLPLRNIPAGTVIHAVELRPGG
GAKLARSAGVSIQLLGKEGTYAALRMPSGEIRRVDVRCRATVGEVGNAEQ
SNINWGKAGRMRWKGKRPTVRGVVMNPVDHPHGGGEGKTSGGRHPVSPWG
KPEGRTRKPNKPSDKLIVRRRRT

Ligand information

>5xym Chain A (length=2665)

aguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaagg
acguaggaggcugcgauaagccucggggagcugucaaccgagcguugauc
cgaggauguccgaauggggaaacccggcacgagugaugucgugucaccag
gcgcuaauauauaggcgucuggggggaacgcggggaagugaaacaucuca
guacccguaggaagagaaaacaaaaugugauuccgugaguaguggcgagc
gaaagcggaggauggcuaaaccggcgggguugugggaugguuagcggaaa
uggcuugggauggccugccguagacggugagagcccgguacgugaaaacc
cgaccccgaguagcagcgggcccguggaaucugcugugaaucugccggga
ccacccgguaagccugaauacuucccagugaccgauagcggauuaguacc
gugagggaauggugaaaaguaccccgggaggggagugaaagaguaccuga
aaccgugcgcuuacaauccgucagagcccucgacuggggugauggcgugc
cuuuugaagaaugagccugcgagucagggacaugucgcgagguuaacccg
ggugggguagccgcagcgaaagcgagucugaauagggcguauccacacaa
gagugugugguguagugguguguucuggacccgaagcggagugaucuacc
cauggccagggugaagcgcggguaagaccgcguggaggcccgaacccacu
uagguugaagacugaggggaugagcuguggguaggggugaaaggccaauc
aaacuccgugauagcugguucuccccgaaaugcauuuaggugcagcgucg
cauguuucuugccggagguagagcuacuggauggccacgucagccaaacu
ccgaaugccgguaaguccaagagugcggcagugggacggcgggggauaag
cuccgugcgucgagagggaaacagcccagaucgccggcuaaggccccuaa
gcgugugcuaaguggaaaaggaugugcagucgugauugugcgccgauaau
guagcggggcucaagcacaccgccgaagccgcggcagccaauuggcuggg
uaggggagcguccugcauccggugaagccgccgagugaucgaguggugga
gggugugggagugagaaugcaggcaugaguagcgauuaggcaagugagaa
ccuugcccgccgaaagaccaaggguuccugggccaggccaguccgcccag
ggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaacg
gguugauauucccguacccguguagcgauggggugacgcaggaagguagc
cguaccggucaggguaauaccgggguaagccuguagggagucgauaggua
aauccgucuggcauccugagaggugaugcauagccgcgaauucggugauc
cuaugcugccgagaaaagccucuagcgacacggcccguaccccaaaccaa
cacagguggucagguagagaauacuaaggcguacgagugaacuaugguua
aggaacucggcaaaaugcccccguaacuucgggagaagggggacccacau
ggcguguaagcgugaguggguggcacaaaccagugagaagcgacuguuua
cuaaaaacacagguccgugcgaagucgcaagacgauguauacggacugac
gccugcccggugcuggaagguuaagaggacccguuaacugugaagcggag
aauuuaagccccaguaaacggcggugguaacuauaaccauccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaauggcguaacgacu
ucucaacugucucaaccauagacucggcgaaauugcacuacgaguaaaga
ugcucguuacgcgcggcaggacgaaaagaccccgggaccuucacuacaac
uugguauuggugcucgagggccucuaaccucggaccguaauccgguucag
ggacagugccugguggguaguuuaacuggggcgguugccuccuaaaaugu
aacggaggcgcccaaagguucccucaaccuggacggcaaucagguguuga
guguaagugcacaagggagcuugacugcgagacggacaugucgagcaggg
acgaaagucgggacuagugauccggcaccucugaguggaaggggugucgc
ucaacggauaaaagguaccccggggauaacaggcugaucuuccccaagag
uccauaucgacgggaugguuuggcaccucgaugucggcucgucgcauccu
ggggcuggagcaggucccaaggguugggcuguucgcccauuaaagcggca
cgcgagcuggguuuagaacgucgugagacaguucggucucuauccgccgc
gcgcgucagaagcuugaggaaaccugucccuaguacgagaggaccgggac
ggacgaaccucugguauaccaguugucccaccaggggcacggcuggauag
ccacguucggacaggauaaccgcugaaagcaucuaagcgggaaaccucuu
ccaagaccaggcuucucacccucuaggagggauaaggccccccgcagacc
acgggauugauagaccagaccuggaagccuaguaauaggugcagggaacu
ggcacuaacggccga

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xym Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.
• Resolution: 3.08 Å
• Binding residue (original residue number in PDB): R4 K7 R13 R14 F21 K31 R35 P36 L37 H38 G39 K40 G42 R43 N44 A45 H46 G47 R48 I49 T50 T51 R52 K54 G55 G56 H58 K59 R60 A61 Y62 R63 K72 V75 K78 Y84 P86 R88 T89 H96 D99 G100 R148 G150 K154 L155 A156 R157 S158 A159 G160 M177 P178 S179 E181 R183 R188 Q201 S202 N205 G207 K208 A209 G210 R211 M212 R213 W214 R218 P219 T220 V221 R222 G223 V224 V225 M226 N227 P228 V229 D230 H231 H233 G235 G236 E237 G238 K239 G243 R244 H245 P246 V247 P249 W250 K252 G255 R256 T257 R258 P260 S264 R272
• Binding residue (residue number reindexed from 1): R3 K6 R12 R13 F20 K30 R34 P35 L36 H37 G38 K39 G41 R42 N43 A44 H45 G46 R47 I48 T49 T50 R51 K53 G54 G55 H57 K58 R59 A60 Y61 R62 K71 V74 K77 Y83 P85 R87 T88 H95 D98 G99 R147 G149 K153 L154 A155 R156 S157 A158 G159 M176 P177 S178 E180 R182 R187 Q200 S201 N204 G206 K207 A208 G209 R210 M211 R212 W213 R217 P218 T219 V220 R221 G222 V223 V224 M225 N226 P227 V228 D229 H230 H232 G234 G235 E236 G237 K238 G242 R243 H244 P245 V246 P248 W249 K251 G254 R255 T256 R257 P259 S263 R271

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:5xym, PDBe:5xym, PDBj:5xym
• PDBsum: 5xym
• PubMed: 28875450
• UniProt: A0QSD4|RL2_MYCS2 Large ribosomal subunit protein uL2 (Gene Name=rplB)