Structure of PDB 6q8y Chain z Binding Site BS01

Receptor Information
>6q8y Chain z (length=874) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPKFFRYISERWPMILQLIEGTQIPEFDNLYLDMNSILHNCTHGNDDDVT
KRLTEEEVFAKICTYIDHLFQTIKPKKIFYMAIDGVAPRAKMNQQRARRF
RTAMDAEKALKKAIENGDEIPKGEPFDSNSITPGTEFMAKLTKNLQYFIH
DKISNDSKWREVQIIFSGHEVPGEGEHKIMNFIRHLKSQKDFNQNTRHCI
YGLDADLIMLGLSTHGPHFALLREEVTFGRRNSEKKSLEHQNFYLLHLSL
LREYMELEFKEIADEMQFEYNFERILDDFILVMFVIGNDFLPNLPDLHLN
KGAFPVLLQTFKEALLHTDGYINEHGKINLKRLGVWLNYLSQFELLNFEK
DDIDVEWFNLVKQQKKLIGSIKPWLMEQLQEKLSPDLPDEEIPTLELPKD
LDMKDHLEFLKEFAFDLGLFITHSKSKGSYSLKMDLDSIEEEFQNRVNSI
RKTIKKYQNATEKTIYNERFERWKHEYYHDKLKFTTDSEEKVRDLAKDYV
EGLQWVLYYYYRGCPSWSWYYPHHYAPRISDLAKGLDQDIEFDLSKPFTP
FQQLMAVLPERSKNLIPPAFRPLMYDEQSPIHDFYPAEVQLDKNGKTADW
EAVVLISFVDEKRLIEAMQPYLRKLSPEEKTRNQFGKDLIYSFNPQVDNL
YKSPLGGIFSDIEHNHCVEKEYISEIRYGLLPNAKLGAEMLAGFPTLLSL
PFTSSLEYNETMVFQQPSKQQSMVLQITDIYKTNNVTLEDFSKRHLNKVI
YTRWPYLRESKLVSLTDGKTIYEYQESNDKKKFGFITKPAETQDKKLFNS
LKNSMLRMYAKQKAVKIGPMEAIATVFPVTGLVRDSDGGYIKTFSPTPDY
YPLQLVVESVVNEDERYKERGPIP
Ligand information
>6q8y Chain 2 (length=1767) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggccggucggauuuccaacggggccuuuccuucuggcuaaccuugagucc
uuguggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguu
caaagcaggcguauugcucgaauauauuagcauggaauaauagaauagga
cguuugguucuauuuuguugguuucuaggaccaucguaaugauuaauagg
gacggucgggggcaucaguauucaauugucagaggugaaauucuuggauu
uauugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaa
ucaagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucu
uaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaaugacc
cacucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguau
ggucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggag
uggagccugcggcuuaauuugacucaacacggggaaacucaccaggucca
gacacaauaaggauugacagauugagagcucuuucuugauuuugugggug
guggugcauggccguucuuaguugguggagugauuugucugcuuaauugc
gauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcug
guuauccacuucuuagagggacuaucgguuucaagccgauggaaguuuga
ggcaauaacaggucugugaugcccuuagacguucugggccgcacgcgcgc
uacacugacggagccagcgagucuaaccuuggccgagaggucuugguaau
cuugugaaacuccgucgugcuggggauagagcauuguaauuauugcucuu
cagcgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacgu
cccugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuua
gugaggccucaggaucugcuuagagaucucagagcggagaauuuggacaa
acuuggucauuuagaggaacuaaaagucguaacaagguuuccguagguga
accugcggaaggaucau
...<<<<<.{.[[[[>>>>><<<<.<<<<<<...<.<...<.........
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>>><...<<<<<<......(((((((...<....>...............
.>>>>>>.....>...<<<<..<<<.....>>>.>>>>....>>>...>>
>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>..
....>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<.......
...>>>.>>.<.<<<..>>>.>....>>............<<<....<<<
.....>>>..>>>..>....>.>.....<<<<<<<<<.<<<....>>>.>
>>>>>.>>>......<<..<...........>..>>.........<<<<<
((......<<<<.....<<..))>>.......>>>>.>>>>>..>>>>>>
>>>>.........<<<[[.....<.<<...<<<.<<....<<<<<<.<<<
<..............>>>>.>>>>>>....<<<<<<..............
.................>>>>>>...<<<<<.<<.......<<...<...
....>..<<<.....>>>....>>......>>.>>..>>>.........<
<...<<<<<<<<.....))))))).>>>>>>>>..>>.....>>....<<
<<<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>......>
.>>>>>>..>>.......<<....>>...>>>>...>>>>>.>>>...>>
>...>>.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>>>
>>>>..........<<<.<<.<<<..<<<<<<<<.<<<........>>>>
>>>>>>>..>>>...<<..]]>>...>>.....>>>.>>>.<<<......
<<<<....>>>>....>>>..]]]].}<<<<<.<<<<<<<..<<.<<<<<
<..<<<.<<<<<<......<<........>>..........<<<<<....
..<<<<<........<<.<<<........>>>.>>......>>>>>...<
<.<<<..<<<<<<<<<....<<<.<<<<<....>>>...<<<......>>
>...>>.>>>....<<<<<.<<..<<<<..<<<<<.<<<<<<....>>>>
>>...>>>>>..>>>>.>>....<<<<<<.....>>>>>>.......>>>
>>....>>>.>>>...>.>>>>>>>.......>>>>>...>>.>>>>.>>
>.....<<<<<<.......<<.....<<..<<<<....>>>>..>>....
>>........>>>>>>...........<<<<<<..........>>>>>>.
.........>>>>>>....<<<<<<<<.......>>>>>>>>......>>
...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<.<
<<..<.<<..<...<<<<<<<..........>>>>>>>...>..>>.>..
>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<<..
>>>>>>>>>>.......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6q8y Structure of the 80S ribosome-Xrn1 nuclease complex.
Resolution3.1 Å
Binding residue
(original residue number in PDB)
D50 E121 I122 K124
Binding residue
(residue number reindexed from 1)
D48 E119 I120 K122
Enzymatic activity
Enzyme Commision number 3.1.13.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004527 exonuclease activity

View graph for
Molecular Function
External links
PDB RCSB:6q8y, PDBe:6q8y, PDBj:6q8y
PDBsum6q8y
PubMed30911188
UniProtP22147|XRN1_YEAST 5'-3' exoribonuclease 1 (Gene Name=XRN1)

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