7D6I

A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb7D6I/pdb

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


• Deposited: 2020-09-30 Released: 2021-10-13 
• Deposition Author(s): Shi, R., Qi, J.X., Gao, G.F., Yan, J.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 0.255 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2

Shi, R., Qi, J.X., Gao, G.F., Yan, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 73.08 kDa 
• Atom Count: 4,768 
• Modelled Residue Count: 627 
• Deposited Residue Count: 666 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	214	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
Heavy chain of GH12-Fab	B	235	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of GH12-Fab	C	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 0.255 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.605	α = 90
b = 150.605	β = 90
c = 121.32	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Shi, R., Qi, J.X., Gao, G.F., Yan, J.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFC0848300

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2021-11-10
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary