8F2X | pdb_00008f2x

Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain

PDB DOI: https://doi.org/10.2210/pdb8F2X/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-11-08 Released: 2024-04-17
Deposition Author(s): Sankhala, R.S., Joyce, G.M.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.324 (Depositor), 0.274 (DCC)
R-Value Work:
0.245 (Depositor), 0.263 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain

Sankhala, R.S., Jensen, J., Modjarrad, K., Nelson, M., Joyce, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 71.6 kDa
Atom Count: 4,862
Modeled Residue Count: 629
Deposited Residue Count: 651
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2123 Fab Heavy chain	B [auth H]	232	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2123 Fab Light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.324 (Depositor), 0.274 (DCC)
R-Value Work: 0.245 (Depositor), 0.263 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.29	α = 90
b = 94.43	β = 90
c = 201.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH-07-2-0067

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.