Structure of PDB 6z6n Chain CB Binding Site BS01

Receptor Information

>6z6n Chain CB (length=846) Species: 9606 (Homo sapiens)

NFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAG
ETRFTDTRKDEQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINL
IDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIK
PVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGN
IMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAERAKKVEDMMKKLWG
DRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEET
AKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPV
TAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYA
FGRVFSGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIE
DVPCGNIVGLVGVDQFLVKTGTITTFEHAHNMRVMKFSVSPVVRVAVEAK
NPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLE
EDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDG
LAEDIDKGEVSARQELKQRARYLAEKYEWDVAEARKIWCFGPDGTGPNIL
TDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVHDVTLHAD
AIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGV
LNRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQC
VFDHWQILPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDNFLDKL

Ligand information

>6z6n Chain L5 (length=3772)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggccggagccccgcggacgcuacgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggagccgccgcagg
ugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggcc
gaaguggagaaggguuccaugugaacagcaguugaacaugggucagucgg
uccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccg
uugcccucggccgaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgcggccggcgccuagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagagguguagaauaa
gugggaggcccccggcgcccccccgguguccccgcgaggggcccggggcg
ggguccgccggcccugcgggccgccggugaaauaccacuacucugaucgu
uuuuucacugacccggugaggcgggggggcgagccccgaggggcucucgc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugacuggggcgguacaccugucaaacg
guaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgug
gagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacag
accgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagca
ggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaag
cguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauc
auugugaagcagaauucaccaagcguuggauuguucacccacuaauaggg
aacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacu
gaugauguguuguugccaugguaauccugcucaguacgagaggaaccgca
gguucagacauuugguguaugugcuuggcugaggagccaauggggcgaag
cuaccaucugugggauuaugacugaacgccucuaagucagaaucccgccc
aggcggaacgauacggcagcgccgcggagccucgguuggccucggauagc
cggucccccgccgggguccggugcggagugcccuucguccugggaaacgg
ggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguu
cguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguc
agcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z6n Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): H27 H108 V137 R162 P723 R726 Y760 N764 R765 V770 R801 S802 G805 K845 N853
• Binding residue (residue number reindexed from 1): H25 H106 V135 R160 P711 R714 Y748 N752 R753 V758 R789 S790 G793 K833 N841

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:6z6n, PDBe:6z6n, PDBj:6z6n
• PDBsum: 6z6n
• PubMed: 32687489
• UniProt: P13639|EF2_HUMAN Elongation factor 2 (Gene Name=EEF2)