9ZDU | pdb_00009zdu

Crystal structure of SARS-CoV-2 RBD in complex with human Ab401 Fab

• PDB DOI: https://doi.org/10.2210/pdb9ZDU/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-11-26 Released: 2026-04-22 
• Deposition Author(s): Fan, C., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

mRNA delivery of a class 1/4 SARS-CoV-2 neutralizing antibody protects against diverse sarbecoviruses in a lethal mouse challenge model

Skelly, A.N., Fan, C., Bjorkman, P.J., Hahn, B.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.02 kDa 
• Atom Count: 5,027 
• Modeled Residue Count: 640 
• Deposited Residue Count: 667 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	212	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ab401 Fab heavy chain	B [auth H]	241	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ab401 Fab light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	F [auth L]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.612	α = 90
b = 83.612	β = 90
c = 217.706	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Fan, C., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01-AI165075
Bill & Melinda Gates Foundation	United States	--

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release