ISDA

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, synthetic construct

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2024-02-21

Release Date:

2025-01-15

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

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Macromolecular Entities

Polymer Type:polypeptide(L)
Description: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)
Description:Spike protein S1
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

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Primary Citation of related structures