7MZF

SARS-CoV-2 receptor binding domain bound to Fab PDI 37

• PDB DOI: https://doi.org/10.2210/pdb7MZF/pdb

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


• Deposited: 2021-05-24 Released: 2021-10-06 
• Deposition Author(s): Pymm, P., Chan, L.J., Dietrich, M.H., Tan, L.L., Tham, W.H.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 71.46 kDa 
• Atom Count: 4,973 
• Modelled Residue Count: 624 
• Deposited Residue Count: 643 
• Unique protein chains: 3

Macromolecules

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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PDI 37 heavy chain	B [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PDI 37 light chain	C [auth L]	214	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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.919	α = 90
b = 147.665	β = 90
c = 146.099	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Pymm, P., Chan, L.J., Dietrich, M.H., Tan, L.L., Tham, W.H.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT2002073

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2021-10-20
  Changes: Database references
• Version 1.2: 2021-10-27
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description