ISDA

Deposition Date 2024-03-04

Release Date 2025-03-12

Last Version Date 2025-03-12

Entry Detail

PDB ID:

8YK4

Keywords:

VIRAL PROTEIN

Title:

Structure of SARS-CoV-2 RBD and antibody NT-108

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)
Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.20 Å

R-Value Free:

0.26

R-Value Work:

0.24

R-Value Observed:

0.24

Space Group:

I 2 2 2

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:antibody NT-108, single chain Fv fragment
Chain IDs:A
Chain Length:282
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:B (auth: C)
Chain Length:215
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:A0A7U3DZD0 Pfam ID:PF09408

Ligand Molecules

Primary Citation

Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108

Anraku, Y, Tadokoro, T, Suzuki, T, Sasaki, J, Hashiguchi, T, Kita, S, Shiwa, N, Iwata, N, Nagata, N, Suzuki, T, Kazuki, Y, Fukuhara, H, Oshimura, M, Sato, A, Sasaki, M, Orba, Y, Sawa, H, Maenaka, K.Show

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Primary Citation of related structures