7F6Y

Complex Structure of antibody BD-503 and RBD-E484K of COVID-19

PDB DOI: https://doi.org/10.2210/pdb7F6Y/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2021-06-26 Released: 2022-06-29
Deposition Author(s): Xu, H., Wang, B., Zhao, T.N., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.253
R-Value Work: 0.198
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.

Xu, H., Wang, B., Zhao, T.N., Liang, Z.T., Peng, T.B., Song, X.H., Wu, J.J., Wang, Y.C., Su, X.D.

(2021) Cell Res 31: 1126-1129

PubMed: 34480123 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-021-00554-1
Primary Citation of Related Structures:
7EJY, 7EJZ, 7EK0, 7F6Y, 7F6Z

Organizational Affiliation

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.

Macromolecule Content

Total Structure Weight: 71.97 kDa
Atom Count: 4,757
Modelled Residue Count: 621
Deposited Residue Count: 660
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth R]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth R]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of BD-503	B [auth H]	222	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of BD-503	C [auth L]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth R] MOL2 format, chain D [auth R] mmCIF format, chain D [auth R]	D [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth R] Interactions & Density Focus chain D [auth R]