Structure of PDB 8bon Chain A Binding Site BS01

Receptor Information
>8bon Chain A (length=1069) Species: 10665,2697049 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVT
WFHAIHVTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLL
IVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTF
EYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQ
GFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVG
YLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNF
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVL
YNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKI
ADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDI
STEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELL
HAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRD
IADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCT
EVNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGA
ENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSN
LLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFN
FSQILPDPSKPSKRSPIEDLLFNKVTFNGLTVLPPLLTDEMIAQYTSALL
AGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFN
SAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLN
DILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATK
MSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTA
PAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDV
VIGIVNNTVYDPLQPELDS
Ligand information
>8bon Chain D (length=18) Species: 32630 (synthetic construct) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
YRRPREQIIIGSLWVFCG
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8bon A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		Q14 W353 P426 D428 T430 P463 F464 R466 E516 L517 L518 H519
Binding residue
(residue number reindexed from 1)		Q1 W335 P408 D410 T412 P445 F446 R448 E498 L499 L500 H501
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0039660 structural constituent of virion
GO:0042802 identical protein binding
GO:0046789 host cell surface receptor binding
GO:0048018 receptor ligand activity
Biological Process
GO:0007165 signal transduction
GO:0019062 virion attachment to host cell
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0019081 viral translation
GO:0039587 suppression by virus of host tetherin activity
GO:0039654 fusion of virus membrane with host endosome membrane
GO:0046598 positive regulation of viral entry into host cell
GO:0046718 symbiont entry into host cell
GO:0046813 receptor-mediated virion attachment to host cell
GO:0052170 symbiont-mediated suppression of host innate immune response
GO:0061025 membrane fusion
GO:0075509 endocytosis involved in viral entry into host cell
GO:0098670 entry receptor-mediated virion attachment to host cell
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0019031 viral envelope
GO:0020002 host cell plasma membrane
GO:0043655 host extracellular space
GO:0044173 host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0044228 host cell surface
GO:0055036 virion membrane

View graph for
Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:8bon, PDBe:8bon, PDBj:8bon
PDBsum8bon
PubMed37339194
UniProtP0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S);
P10104

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