ISDA

Deposition Date 2024-02-21

Release Date 2025-01-15

Last Version Date 2025-01-15

Entry Detail

PDB ID:

8YDP

Keywords:

VIRAL PROTEIN/INHIBITOR

Title:

Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
synthetic construct (Taxon ID: 32630)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.30 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 31

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:SARS-CoV-2 inhibiting peptide Ce9
Chain IDs:A, C
Chain Length:39
Number of Molecules:2
Biological Source:synthetic construct

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:B, D
Chain Length:230
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Ligand Molecules

GOL

NAG

Primary Citation

Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology

Nakamura, S, Tanimura, Y, Nomura, R, Suzuki, H, Nishikawa, K, Kamegawa, A, Numoto, N, Tanaka, A, Kawabata, S, Sakaguchi, S, Emi, A, Suzuki, Y, Fujiyoshi, Y.Show

To Be Published ? ? ? (?)

Primary Citation of related structures