Structure of PDB 8k2a Chain Sc Binding Site BS01

Receptor Information

>8k2a Chain Sc (length=385) Species: 9606 (Homo sapiens)

LSSAYVDSHKWEAREKEHYCLADLASLMDKTFERKLPVSSLTISRLIDNI
SSREEIDHAEYYLYKFRHSPNCWYLRNWTIHTWIRQCLKYDAQDKALYTL
VNKVQYGIFPDNFTFNLLMDSFIKKENYKDALSVVFEVMMQEAFEVPSTQ
LLSLYVLFHCLAKKTDFSWEEERNFGASLLLPGLKQKNSVGFSSQLYGYA
LLGKVELQQGLRAVYHNMPLIWKPGYLDRALQVMEKVAASPEDIKLCREA
LDVLGAVLKALTSADGASEEQSQNDEDNQGSEKLVEQLDIEETEQSKLPQ
YLERFKALHSKLQALGKIESEGLLSLTTQLVKEKLSTCEAEDIATYEQNL
QQWHLDLVQLIQREQQQREQAKQEYQAQKAAKASA

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): K64 P66 W102 Y103 L104 R105 R392 Q396 K411
• Binding residue (residue number reindexed from 1): K35 P37 W73 Y74 L75 R76 R363 Q367 K382

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0097177 mitochondrial ribosome binding

Biological Process

• GO:0006417 regulation of translation
• GO:0008283 cell population proliferation
• GO:0032543 mitochondrial translation
• GO:0070131 positive regulation of mitochondrial translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• 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: Q92552|RT27_HUMAN Small ribosomal subunit protein mS27 (Gene Name=MRPS27)