Structure of PDB 8y0x Chain CB Binding Site BS02

Receptor Information

>8y0x Chain CB (length=755) Species: 9606 (Homo sapiens)

NFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAG
ETRFTDTTAISLFYELSENDLNFIKQSKDGAGFLINLIDSPGHVDFSSEV
TAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALL
ELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFG
SGLHGWAFTLKQFAEMYVAKFAERAKKVEDMMKKLWGDRYFDPANGKFSK
SATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKLDIKLDS
EDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPVTAQKYRCELLYEG
PPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLVSTGL
KVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGV
DQFLVKTGTITTFEHAHNMRDPVVSYRETVSEESNVLCLSKSPNKHNRLY
MKARPFPDGLAEDIDKGEVSARQELKQRARYLAEKYEWDVAEARKIWCFG
PDGTGPNILTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFD
VHDVTLHADAIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPE
QVVGGIYGVLNRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSN
TGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDN
FLDKL

Ligand information

>8y0x Chain S2 (length=1739)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuuaacgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgcccuc
ucggccggggcccgaagcguuuacuuugaaaaaauuagaguguucaaagc
aggcccgagccgccuggauaccgcagcuaggaauaauggaauagaccgcg
guucuauuuuguugguuuucggaacugaggccaugauuaagagggacggc
cgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcgca
agacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaaga
acgaaagucggagguucgaagacgaucagauaccgucguaguuccgacca
uaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgccgg
gcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguugc
aaagcugaaacuuaaaggaauugacggaagggcaccaccaggaguggagc
cugcggcuuaauuugacucaacacgggaaaccucacccggcccggacacg
gacaggauugacagauugauagcucuuucucgauuccgugggugguggug
cauggccguucuuaguugguggagcgauuugucugguuaauuccgauaac
gaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucggc
gucccccaacuucuuagagggacaaguggcguucagccacccgagauuga
gcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcgcu
acacugacuggcucagcgugugccuacccuacgccggcaggcgcggguaa
cccguugaaccccauucgugauggggaucggggauugcaauuauucccca
ugaacgaggaauucccaguaagugcgggucauaagcuugcguugauuaag
ucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguuu
agugaggcccucggaucggccccgccggggucggcccacggcccuggcgg
agcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagucgu
aacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0x The global structure of dormant ribosome
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): R633 K667 I714 G717 G719 Q720
• Binding residue (residue number reindexed from 1): R530 K564 I611 G614 G616 Q617

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019901 protein kinase binding
• GO:0043022 ribosome binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002244 hematopoietic progenitor cell differentiation
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0045727 positive regulation of translation

Cellular Component

• GO:0005576 extracellular region
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0016235 aggresome
• GO:0034774 secretory granule lumen
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1904813 ficolin-1-rich granule lumen
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0x, PDBe:8y0x, PDBj:8y0x
• PDBsum: 8y0x
• PubMed: 38698775
• UniProt: P13639|EF2_HUMAN Elongation factor 2 (Gene Name=EEF2)