Structure of PDB 6zlw Chain E Binding Site BS01

Receptor Information

>6zlw Chain E (length=262) Species: 9606 (Homo sapiens)

ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNR
LKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRL
IYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPD
PLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERH
PGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE
RDKRLAAKQSSG

Ligand information

>6zlw Chain 2 (length=1665)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucucucucggccgaagcguuuacuuugaaaaaauuagagug
uucaaagcaggccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgaccggucggcguaa
cuucuuagagggacaaguggcguucagccacccgagauugagcaauaaca
ggucugugaugcccuuagauguccggggcugcacgcgcgcuacacugacu
ggcucagcguguccuacgccggcaggcgcggguaacccguugaaccccau
ucgugauggggaucggggauugcaauuauuccccaugaacgaggaauucc
caguaagugcgggucauaagcuugcguugauuaagucccugcccuuugua
cacaccgcccgucgcuacuaccgauuggaugguuuagugaggcccucgga
ucggccccgccggggugcccuggcggagcgcugagaagacggucgaacuu
gacuaucuagaggaaguaaaagucguaacaagguuuccguaggugaaccu
gcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zlw Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): R3 G4 K6 K7 H8 K10 R11 V12 K16 M19 D21 K22 L23 T24 V26 F27 A28 P29 R30 T33 G34 K37 L38 R49 T57 G58 K62 M66 K75 R77 K106 R108 K128 V131 K134 G135 V140 A144 R145 T146 R148 H201 P202 G203 A219 R221 I248 R255
• Binding residue (residue number reindexed from 1): R2 G3 K5 K6 H7 K9 R10 V11 K15 M18 D20 K21 L22 T23 V25 F26 A27 P28 R29 T32 G33 K36 L37 R48 T56 G57 K61 M65 K74 R76 K105 R107 K127 V130 K133 G134 V139 A143 R144 T145 R147 H200 P201 G202 A218 R220 I247 R254

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0008284 positive regulation of cell population proliferation
• GO:0042274 ribosomal small subunit biogenesis
• GO:0045727 positive regulation of translation

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:0032040 small-subunit processome
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zlw, PDBe:6zlw, PDBj:6zlw
• PDBsum: 6zlw
• PubMed: 32680882
• UniProt: P62701|RS4X_HUMAN Small ribosomal subunit protein eS4, X isoform (Gene Name=RPS4X)