9C6Y | pdb_00009c6y

Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab

PDB DOI: https://doi.org/10.2210/pdb9C6Y/pdb

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

Deposited: 2024-06-10 Released: 2025-10-08
Deposition Author(s): Buchman, C.D., Crowe, J.E.
Funding Organization(s): Defense Advanced Research Projects Agency (DARPA), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants

Zost, S.J., Buchman, C.D., Crowe, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 146.1 kDa
Atom Count: 10,096
Modeled Residue Count: 1,296
Deposited Residue Count: 1,314
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of COV2-3906 Fab	A, C	225	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of COV2-3906 Fab	B, D	216	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
Spike protein S2'	E, F	216	Severe acute respiratory syndrome coronavirus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain E Focus chain F	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	5		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain M [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain M [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain M [auth E]	M [auth E], Q [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth E] Focus chain Q [auth F] Interactions & Density Focus chain M [auth E] Focus chain Q [auth F]
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain N [auth E] MOL2 format, chain R [auth F] MOL2 format, chain N [auth E] mmCIF format, chain R [auth F] mmCIF format, chain N [auth E]	N [auth E], R [auth F]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain N [auth E] Focus chain R [auth F] Interactions & Density Focus chain N [auth E] Focus chain R [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain S [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain S [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B], O [auth E], P [auth E], S [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth E] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth E] Focus chain P [auth E] Focus chain S [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth B]	K [auth B], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.971	α = 90
b = 170.851	β = 90
c = 231.543	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Buchman, C.D.

Crowe, J.E.

Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	HR0011-18-2-0001
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI157155