Structure of PDB 6th6 Chain BC Binding Site BS01

Receptor Information

>6th6 Chain BC (length=237) Species: 69014 (Thermococcus kodakarensis KOD1)

GKSLIQQRRGKGTTTFRAPSHRYRGAVRYVPLNLVQERTLRGVVEEILHD
PGRTAPVARVKFEDGTKKLIIAPEGVLVGQEIYIGPEAPIAIGNTLPLAK
IPEGTYVYDIEGVPGDGGKYVRAGGTYALVVSREKDKVIVQLPSGELKAF
NPMCRATIGVVAGGGRLEKPIVKAGKAYYIAKARNRFWPKPRGVKMNAVN
HPHGGKEHHIGRPSTVSRRAPPGRKVGHIAARRTGRR

Ligand information

>6th6 Chain BA (length=2934)

cccgguggcaacuaagccgccugguggauggcucggcucggggcgccgac
gaagggcguggcaagcugcgauaagccccggcgaggcgcaggcagccguc
gaaccggggaugcccgaaugggaccucccgcggcuugccgcacucccagu
cgggagggggaacgcggggaauugaaacaucuuaguacccgcaggaaaag
aaagcaaaagcgaugccguuaguaggggcgaccgaaagcggcacagggca
aacugaaccccgggccgaaagguucgggggaugugguguuguagggcccg
cggaggagcccugggggcgaagccgaaguccgcuggaacgcggcgccgga
gagggugaaagccccguaggcguaagcccccgagcuccugcggugucccu
gaguaccgucggucggauauccggcgggaagcugggaggcaucggcuccc
aacccuaaauacgucccgagaccgauagcgaacuaguaccgugagggaaa
gcugaaaagcaccccgggaggggggugaaaagagccugaaaccaggcggc
gauaggagggugcggcccgaaaggguugacccuccccgaaggaaacacgg
gcgaccguggaguacgaggggaggugaccgggguugcaccguccgucuug
gaucacggggcagggaguucacccgagcggcgagguuaagggggucaacc
ccgaagccgcagggaaaccgacagguccgcagcccguagggcgagggacg
gggugugaaagcgcccggagucgcucgggugagacccgaagccggucgau
cuagcccggggcagggugaagucccucaacagagggauggaggcccgcua
ggggugcugacgcgcaauucgcucccgugaccccgggcuaggggugaaag
gccaaucgaggccggcgauagcugguucccgccgaauuaucccccaggau
agcccggccggagguaggcagugggguagagcacugauuggggguuuagg
gggcgaaagccuccggcucccugucaaacuccgaacccacugccgccgua
gauggccggaguaggggggcgguguaagccgucacccgagaggggaacaa
cccagaccgggguuaaggccccaaagugccggcuaaguguuacuccaaag
ggugucccuggccuuagacagcggcccgucgaggucaggggccccgaaaa
uggacggggcuuaagccggccgccgagaccccggcgcacggaccgauugg
uccgugaucggguaggcgggcgugccgauggggcggaagccgggccguga
gguccgguggacccgucgguauugcggauccugccgggaguagcagcaua
gccgggugagaaucccggccgccguaggggccaggguuccacggcaaugu
ucgucagccguggguuagucgguccuaacccgacccguaacucggcgucg
gggaaagggaaacggguuuauauucccguaccgcggugguaggugcggca
acgcaagcccgaggggugacgccucgggguaggcggaccgguccacaagg
ccggcuaagcguauaagcccggggagugccguaauggcgagaaccgggug
aaagcgcgaauggccucccguaagggggguuccgccgaucccuggggccc
gugaaaagccccucgggaacgauccaccgcgaccguaccgagaaccgaca
cuggugccccugggugagaagccuaaggcgugucgggggaaacccagccg
agggaacucggcaaauuggccccguaacuucgggagaaggggugccugcg
gguguguaacccgcaggucgcagugacuaggggggcccgacuguuuagua
aaaacacaggucccagcuagcccgaaaggguuuguacuggggccgacgcc
ugcccagugccgguaugugaagcccggguacaaccgggugaagcaccggu
aaacggcggggguaacuauaacccucuuaagguagcgaaauuccuugucg
guuaaaugccgaccugcaugaauggcguaacgagguccccacuguccccg
gcuggggcccggcgaaaccucugccaggcgcauaugccugggaccuccgg
ugggaagcgaagaccccauggagcuuuacugcagccugccguugccguac
ggcggggggugcgcagcguaggcgggaggcgucgaagcccgcccuccggg
gcggguggagccgcccaugagacaccgcccacccucugccguacggcuaa
cccgcggaagcggggacagcgguaggugggcaguuuggcuggggcggcac
acccucgaaaagguaucgagggugcccuaaggucggcucaggcgggucag
gaauccgccguagagugcaagggcaaaagccggccugacuggacccguaa
cagaggcggguccagccgcgaaagcguggccuagcgaaccccugugccuc
cccggugggggccagggaugacagaaaagcuacccuggggauaacagagu
cgucucgggcgagagcccauaucgaccccgaggcuugcuaccucgcuguc
ggcucuucccauccuggcccugcagcaggggccaaggguggggguguuca
cccauuaaaggggaacgugagcuggguuuagaccgucgugagacaggucg
gaugcuaucuaccggagguguuggccgccugaggggaaggcucccccagu
acgagaggaacagggagccgcggccucuggucuaccgguuguccuacagg
gcauagccgggcagcuacgccgcagccgauaaggccugaaagcaucuaag
gccgaagcggcccccgaaaacaggcggccaccgagggcccgggaagaaga
cccgguugauggggcggggauguaagcgggaagggaaaccgacccguuca
gucugccgcucccaacagcccgagugcuaccggg

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>>>>....<<<<.<..<<<<<<.....<<<<...>>>>.....>>>>>>.
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.......>>>>>>>>>>......>>>>>>>>>>>>..>>.....<<....
..>>...>>>.<<<<.....>>>>..>>>>...<<<<.....<<<<<<<<
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<<<.....>>>>>>>>>>............<<<<<<<<<..<<<......
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<<<<..<<<<..........<<<<<..<<<......<<<<<<.<<...>>
>>>>>>...>>>............>>>>>.>.>>>.>>>>>>>>>>>...
<<<<<....>>>>>....>>>>>>>>>..>>>>>.....<.....>....
<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<....
...>>>>>>.....<<...(((>>....>>>>>>>...<<<<<<<<<<..
.....>>>>>>>>>>.<<<....>>>.>>))).......<<<<<.<<<<<
.>>>>>>>>>>>>>>>>..........>>>>..]]>>>>.......<<<<
.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<
<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>..<<<.......
>>>......>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>.
...]]..>>>>>>>>>>>....<<<<<<<<..<<<<..<<<<<<<.....
............>>>>>>><<<<<...<<<<...<<<<<<<<<<}...>>
>>>..>>>>>...>>>>.>>>>>.<<<<.<..<<<<<...........>>
>>>...>>>>>>>>>>......>>>>>>>.....<<<<<<<<<.......
>>>>>....<<<<<<<<<<<<....<<<<<..<<....>>..>>>>>...
>>>>.>>>>>.>>>...>>>>...>>>>>>>>.>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6th6 Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): G2 K3 S4 Q7 Q8 R9 R10 G11 K12 T14 T15 T16 S21 H22 R23 A27 R29 H50 R54 K120 Y121 V122 R123 A124 G125 G126 L143 S145 E147 K149 G166 R167 K170 I172 V173 K174 A175 G176 K177 Y180 I181 R187 W189 P190 K191 R193 G194 V195 K196 M197 N198 V200 N201 H204 K207 E208 H209 H210 I211 G212 R213 P214 S215 T216 R219 R220 P222 P223 G228 H229 I230 A232 R233 R234 T235 G236 R237
• Binding residue (residue number reindexed from 1): G1 K2 S3 Q6 Q7 R8 R9 G10 K11 T13 T14 T15 S20 H21 R22 A26 R28 H49 R53 K119 Y120 V121 R122 A123 G124 G125 L142 S144 E146 K148 G165 R166 K169 I171 V172 K173 A174 G175 K176 Y179 I180 R186 W188 P189 K190 R192 G193 V194 K195 M196 N197 V199 N200 H203 K206 E207 H208 H209 I210 G211 R212 P213 S214 T215 R218 R219 P221 P222 G227 H228 I229 A231 R232 R233 T234 G235 R236

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• 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:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6th6, PDBe:6th6, PDBj:6th6
• PDBsum: 6th6
• PubMed: 32555463
• UniProt: Q5JDH2|RL2_THEKO Large ribosomal subunit protein uL2 (Gene Name=rpl2)