Structure of PDB 8k2a Chain SO Binding Site BS01

Receptor Information

>8k2a Chain SO (length=164) Species: 9606 (Homo sapiens)

DPPPSTLLKDYQNVPGIEKVDDVVKRLLSLEMANKKEMLKIKQEQFMKKI
VANPEDTRSLEARIIALSVKIRSYEEHLEKHRKDKAHKRYLLMSIDQRKK
MLKNLRNTNYDVFEKICWGLGIEYTFPPLYYRRAHRRFVTKKALCIRVFQ
ETQKLKKRRRALKA

Ligand information

>8k2a Chain S1 (length=928)

auagguuugguccuagccuuucuauuagcucuuaguaagauuacacaugc
aagcauccccguuccagugaguucacccucuaaaucgaucaaaaggaaca
agcaucaagcacgcagcaaugcagcucaaaacgcuuagccuagccacacc
cccacgggaaacagcagugauuaaccuuuagcaauaaacgaaaguuuaac
uaagcuauacuaaccccaggguuggucaauuucgugccagccaccgcggu
cacacgauuaacccaagucaauagaaccggcguaaagaguguuuuagauc
acaauaaagcuaaaacucaccugaguuguaaaaaacuccaguugacacaa
aauagacuacgaaaguggcuuuaacauaucugaacacacaauagcuaaga
cccaaacugggauuagauaccccacuaugcuuagcccuaaaccucaacag
uucaacaaaacugcucgccagaacacuacgagccacagcuuaaaacucaa
aggaccuggcggugcuucauaucccucuagaggagccuguucuguaaucg
auaaaccccgaucaaccucaccaccucuugcucagccuauauaccgccau
cuucagcaaacccugaugaaggcuacaaaguaagcgcaaguacccacgua
aagacguuaggucaagguguagcccaugagguggcaagaaaugggcuaca
uuuucuaccccagaaacgauagcccuuaugaaauaagggucgaaggugga
uuuagcaguaaacuaagaguagagugcuuaguugaacagggcccugaagc
gcguacacaccgcccgucacccuccucaaguauacuucaaaggacaauua
acuaaaaccccuacgcauuuauauagaggagacaagucguaacaugguaa
guguacuggaaagugcacuuggacgaac

..((((..<<<<<<.)))).<<<<<<.<<..<<<<<<<<....<<<.<<<
..<......>......<<........<<<.<..<<..>>.>..>>>...<
<<<....<<...<<<....>>>..>>......>>>>.<<...>>.>>.<<
<....>>>.....>>>>>>.........<<<....<<<<....>>>>..>
>>..>>.>>>>>>.....<<<<<<<<.....(((.....((.>>>))...
....)))..>>>>>..>>.>>>>>>...<<<((.....<<<<..<<<<..
....<<<<<<......<<<.<<<.<<<......>>>..>>>.>>>.....
........<<....>>.>>>>>>.....>>>>...>>>>....<<<<<<.
..<<...<<<<.<.....>.>>>>...>>>>>>>>..........<.<<<
<<..))..>>>>>.>.>>>.<<.......<<<<....>>>>.....>>..
>>>>>><<<<<.<<<<<<<...<<<.<<<<<..<<<<<<<<<<.....<<
........>>..........<<<<<<<.......<<.<<<..<<<<<<..
.....<<..<<<<<.....>>>.......>>..>>.....<<<....>>>
.........>>>...>>>>>>>>....>>>>>>>..>>.>>>>>>>>...
..<<<<.....>>>>.<....<<<<<<<.....>>>>>>>....>.....
>>>>>.....<<<<<<<.........>>>>>>>.....>>>...>>>>>>
>>>>.>>....<..<<.<...<<<<<<..<<<<<......<<<....<<.
....>>...>>>.......>>>>>.>>>>>>....>.>>...>.....<<
<<<<<<<....>>>>>>>>>........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8k2a Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K100 K101 R123 R128 K135 Y139 H142 H146 K148 D149 K150 H152 K153 R154 Y155 M158 S159 D161 Q162 K165 K168 Y195 Y196 R197 R198 H200 R201 R202 F203 K206 C210 F214 R225
• Binding residue (residue number reindexed from 1): K35 K36 R58 R63 K70 Y74 H77 H81 K83 D84 K85 H87 K88 R89 Y90 M93 S94 D96 Q97 K100 K103 Y130 Y131 R132 R133 H135 R136 R137 F138 K141 C145 F149 R160

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005759 mitochondrial matrix
• GO:0005761 mitochondrial ribosome
• GO:0005763 mitochondrial small ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2a, PDBe:8k2a, PDBj:8k2a
• PDBsum: 8k2a
• PubMed: 38942792
• UniProt: P82914|RT15_HUMAN Small ribosomal subunit protein uS15m (Gene Name=MRPS15)