Structure of PDB 6w6l Chain 1 Binding Site BS01

Receptor Information

>6w6l Chain 1 (length=426) Species: 9606 (Homo sapiens)

FLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIM
SSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGD
TPKDRALFNGAQKLFGMIITIGQSIVYVMSGICLLITIQLFVAGLIVLLL
DELLQKGYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIA
LFHLLATRTDKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDL
PIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSARFPVG
GLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKD
VAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLADFLG
AIGSGTGILLAVTIIYQYFEIFVKEQ

Ligand information

>6w6l Chain t (length=3510)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgggcgggggaccgucccccggaccggcgaccggccgccg
ccgggcgcauuuccaggcggugcgccgcgaccggcuccgggacggcuggg
aaggcccggcggggaagguggcucggggcccccgaguguuacagcccccc
cggcagcagcacucgccgaaucccggggccgagggagagacccgucgccg
cgcucuccccccugggggggccgggccaccccucccacggcgcgaccgcu
cucccagggggcggggcggacuguccccagugcgccccgggcgggucgcg
ccgucgggcccggggggccacgcgcgcgucccccgaagggggggacggcg
gagagcgcacggggucggcggcgacgucggcuacccacccgacccgucuu
gaaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacg
aaagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccga
ggugggaucccgaggccucuccaguccgccgaggggcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcccacgcaguuuuauccgguaaag
cgaaugauuagaggucuuggggccgaaacgaucucaaccuauucucaaac
uuuaaauggguaagaagcccggcucgcuggcguggagccgggguggaaug
cgagugccuagugggccacuuuugguaagcagaacuggcgcugcgggaug
aaccgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccag
aaaagguguugguugauauagacugccgaaucaacuagcccugaaaaugg
auggcgcuggagcgucgggcccauacccggccgucgccggcgucgagagu
ggacgggagcggcggcccggagccccgcggacgcuacgccgcgacgagua
ggagggccgcugcggugagccuugaagccuagggcgcgggcccgggugga
gccgccgcaggugcagaucuuggugguaguagcaaauauucaaacgagaa
cuuugaaggccgaaguggagaaggguuccaugugaacagcaguugaacau
gggucagucgguccugagagaugggcgagcgccguuccgaagggacgggc
gauggccuccguugcccucggccgaucgaaagggagucggguucagaucc
ccgaauccggaguggcggagaugggcgccgcgaggcguccagugcgguaa
cgcgaccgaucccggagaagccggcgggagccccggggagaguucucuuu
ucuuugugaagggcagggcgcccuggaauggguucgccccgagagagggg
cccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucg
cuggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgu
acccauauccgcagcaggucuccaaggugaacagccucuggcauguugga
acaauguagguaagggaagucggcaagccggauccguaacuucgggauaa
ggauuggcucuaagggcuggcagccgacuuagaacuggugcggaccaggg
gaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggu
guugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaagg
uagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaacg
agauucccacugucccuaccuacuauccagcgaaaccacagccaagggaa
cgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacucu
agucuggcacggugaagagacguuuuuucacugacccggugaggcggggg
ggcgagcccgaggggcucucgcuucuggcgccaagcgcccgcccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucgccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccgguccccgccggggguccggugcggagugcccuu
cguccugggaaaccucgcccgucacgcaccgcacguucguggggaaccug
gcgcuaaaccauucguagacgaccugcuucugggucgggguuucguacgu
agcagagcagcucccucgcugcgaucuauugaaagucagcccucgacaca
aggguuuguc

.........................<<<<<<.....<<....>>......
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>..>...<.<<..<<.....<.<.<.........<<<<........<.<.
.......>.>..................................>>>>..
..>..>>....>>..>>.>.......<<<<<<<........>>>>>>>..
...(((((..<<<<<<)))))..]]]........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<........
..<<.<.<<<<....<<.<..<..<.........<....<<.......<<
<<.<<<..<<<<..>>>>>>>>>>>..>>....>..........>..>..
>.>>....>>>>.>.>>.....<<<<<<<<.<<<<<<<<<<.<<<.....
...<<<.<<.<<<.......<<<<<<<<.>>>>>>>>........>>>.>
>>>>...........>>>...>>>>>>>>>>...................
......<<<<<<..>>>>>>....<<.......<<...<....<.<<<<<
...<<...>>.<<<<<<<.<<<<....>>>>.>>>>>>>>>>>>.>....
>....>>.........>>..........<<<<<<....>>>>>>......
..............>>>.>>>>>....>>>...>>>>>>>>..<<<<...
.....>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<......
..>>>>.....>>>...<<....>>...<<<<<<<......>>>>>>>..
<<<<<..<<<...<.....[[.......>...>>>...>>>>>.<<<<<<
<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.
<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>
>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>
>...<<.......>>......>>>>>>......>.>>..<<<<<<....<
.<<<....>>>.><<.<<<<<<<........<<<.<<<<<<<<<...<<<
....<<...<.<<<<..<.<<<.........>>>.>>>>>.>...>>..>
.>>...>>>>>>>....<<<<<<<<.........>>>>>>>>....>>>>
>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>....<<<....
..>>>...<<<<<<<...<<<(((.......<<<<<.....<<.......
...<<<.<<<<<<<<<<............>>>>>>>>>>>>>........
..))).>>...>>>>>..>>>...>>>>>>><<<<<<.<...........
.....]].....<.....>...................>.>>>>>>....
>>>>>>...<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...
>>>>>>>>>>........>>>>>><<<....<<.....<<<<<<......
.>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>
>>....((<<<<<<...<<....<<<....>>>..........<<.<<<<
<<<<<...>>>>>>>>>>>......>>....>>>..<<<<<........>
>>>>))<<<<....<<<<<...<<<<<<<....>>>>>>>...<<<....
>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..{{{..>
>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>
>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>...>>>>>>>
>>>>>.........>>>>>>>..>..........>>.>>>.>>>>.>>>.
.>>.....<<......>>>>>>>.<<<<.....>>>>..>>>....<<<<
.....<<<<<<<.<<.........<.....<<<<<...............
>>>>><<.<<<<<<<<<<<.>>>>>..>>>>>>.>>............<<
<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>>
......>>>>>>>...<<..<<<..<<<<<<....<<<...<.<<<<...
.>>>>.>...>>>.>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<.......>>>>>.....>.....>>....>>
.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>>>....<<<<<....
....>>>>>....[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<
.<<<<<<<<<.<<<<<<<<<..>>>>>>>>>...<<<<<.....<<<<..
.<.<<...........>>>...............<<<<<<<......>>>
>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>...<<<.....>>
>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.
......>>>>>>.....<<...(((>>....>>>>>>>...<<<..<<<<
.......>>>>..>>><<<<....>>>>>>))).......((((((..((
(..>>>>>>.)))))))))..........]]]]..}}]]]].......<<
.<...<<<<<<...<<.......>>...>>>>>>....>.>.>.......
<<<<<.<<<<<<..<.<.<<<<<......>>>>>.>...>.<<<......
...>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>
>....}}..}}}.]]]]].....<<<<<<.<..<<<..<.<<<<<.....
............>>>>>.><<<<....<<<<....<<.<<<<<<<}}}.>
>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<...........>
>>>>...>>>>>.>>>...>.>>>>>>......<<<<<<.<<..<<<..<
..<.............<.<<<<....>>>>.>.............>....
<<<..<<<<........>>>>..>>>..........>...>>>...>>>>
>>>>.<<<<<.<.............>.....<.<<<<<<<.<<.....<<
<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>.>.
..>>>>>...

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6w6l An ER translocon for multi-pass membrane protein biogenesis.
• Resolution: 3.84 Å
• Binding residue (original residue number in PDB): K268 R402 R405
• Binding residue (residue number reindexed from 1): K253 R363 R366

Gene Ontology

Molecular Function

• GO:0005048 signal sequence binding
• GO:0005262 calcium channel activity
• GO:0005515 protein binding
• GO:0008320 protein transmembrane transporter activity
• GO:0043022 ribosome binding

Biological Process

• GO:0006613 cotranslational protein targeting to membrane
• GO:0006614 SRP-dependent cotranslational protein targeting to membrane
• GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation
• GO:0006620 post-translational protein targeting to endoplasmic reticulum membrane
• GO:0007029 endoplasmic reticulum organization
• GO:0015031 protein transport
• GO:0031204 post-translational protein targeting to membrane, translocation
• GO:0039019 pronephric nephron development
• GO:0045047 protein targeting to ER
• GO:0045048 protein insertion into ER membrane
• GO:0070588 calcium ion transmembrane transport

Cellular Component

• GO:0005783 endoplasmic reticulum
• GO:0005784 Sec61 translocon complex
• GO:0005789 endoplasmic reticulum membrane
• GO:0016020 membrane

External links

• PDB: RCSB:6w6l, PDBe:6w6l, PDBj:6w6l
• PDBsum: 6w6l
• PubMed: 32820719
• UniProt: P61619|S61A1_HUMAN Protein transport protein Sec61 subunit alpha isoform 1 (Gene Name=SEC61A1)