Structure of PDB 6zmt Chain D Binding Site BS01

Receptor Information
>6zmt Chain D (length=218) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLK
IMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAP
VPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKE
TVFTKSPYQEFTDHLVKT
Ligand information
>6zmt Chain 2 (length=1569) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucucucucggccgaagcguuuacuuugaaaaaauuagagug
uucaaagcaggccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucaccauaaacgaugccgaccggcgaugcggcggcguuau
ucccaugacccgccgggcagcuuccgggaaaccaaagucuuuggguuccg
gggggaguaugguugcaaagcugaaacuuaaaggaauugacggaagggca
ccaccaggaguggagccugcggcuuaauuugacucaacacgggaaaccuc
acccggcccggacacggacaggauugacagauugauagcucuuucucgau
uccgugggugguggugcauggccguucuuaguugguggagcgauuugucu
gguuaauuccgauaacgaacgagacucuggcaugcuaacuaguuacgcga
ccggucggcguaacuucuuagagggacaaguggcguucagccacccgaga
uugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcg
cgcuacacugacuggcucagcguguccuacgccggcaggcgcggguaacc
cguugaaccccauucgugauggggaucggggauugcaauuauuccccaug
aacgaggaauucccaguaagugcgggucauaagcuugcguugauuaaguc
ccugcccuuuguacacuacuaccgauuggaugguuuagugaggcccucgg
aucggccccgccggggugcccuggcggagcgcugagaagacggucgaacu
ugacuaucuagaggaagua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<.........<<.....<<.<<<...
..>>>.>>......>>.........<<<<...<<<<<<....>>>>>>..
.>>>><<..<<<<<...<......>..>>>>>......>>...<<<<.<<
<..>>>>>>>.>>.>>>...>>..>.>>>.<<<....<<<....<<<<<<
<.........>>>>>>>>>>......>>>...<<<.<<<<....>>>>..
..>>>.>>.<<.<<<..........>>>.>>.<.<<....>>.>...>>>
>>>.........<<<....<<<<...>>>>..>>>..>...>>.>.....
<<<....<<.<<<....>>>..>>.....>>>......<<..<.......
....>..>>.........<<<<<((......<<<<.....<<..))>>..
.....>>>>.>>>>>..>>>>>>.>>>.........<.<((.....<.<<
...<<<.<<...<<.<<<..>>>>>...<<<<<<.<.......<<...<.
......>.<<<<.>>>>...>>......>.>>>..>>>........<.<<
.<<<<<<<...............>>>>>>>.>>.>....>>....<<<<<
<..<...<<<<..<<<.<<<<<<<<...<<<......>>>......>>>>
>>>>.>>>.......<<....>>...>>>>..>..>>>.>>>...>>>..
.>>.>....<<.>>..........<<<.<<.<<<..<.<<<<<<.<<<<<
....>>>>>>>>>>>.>..>>>...<<..))>>...>>.....>>>.>.>
.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<
..<<..<<<<<..<<<.<<<<<<......<<........>>.........
.<<<<<.<....<<<<<<.......<<.<<<........>>>.>>.....
>>>>>>.<.<<.<<<..<<.<<<<<<....<<<.<<<<<....>>>...<
<<......>>>...>>.>>>....<<<...<...<<<<..<<<<<<<<<<
<..>>>.>>>>>>>>..>>>>..>.....<<<<<.....>>>>>......
..>>>....>>>.>>>.....>>>>>>>>....>.>>>>>...>>.>>>>
.>>>.....<<.<<<........<.<<<.<<<<....>>>>.>>>....>
.........>>>.>>......<.....<<<<<..........>>>>>...
..>.....>>>>>.....<<<<<<<<.......>>>>>>>>......>>.
..>>>>>>>>>>.>>.<<<<.<<....<<<<<<<<.<<<..<<<<.<<..
.<<<<<<<<<<<<<<<..>>>>>>>>>.>.>>>>>...>>.>>>>..>>>
.>>>>>>>>...>>.>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6zmt Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		M110 V112 Q113 K114 Q115 R117 K125 T185 R187 G189 S190 L192 R194 V205 S206 A207 Y223 T224 A226 R227 C229 T230 T232 N235 K238 Y250
Binding residue
(residue number reindexed from 1)		M52 V54 Q55 K56 Q57 R59 K67 T127 R129 G131 S132 L134 R136 V147 S148 A149 Y165 T166 A168 R169 C171 T172 T174 N177 K180 Y192
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0017134 fibroblast growth factor binding
GO:0019899 enzyme binding
GO:0045296 cadherin binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0051443 positive regulation of ubiquitin-protein transferase activity
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005925 focal adhesion
GO:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6zmt, PDBe:6zmt, PDBj:6zmt
PDBsum6zmt
PubMed32680882
UniProtP15880|RS2_HUMAN Small ribosomal subunit protein uS5 (Gene Name=RPS2)

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