3NK3

Crystal structure of full-length sperm receptor ZP3 at 2.6 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NK3/pdb

• Classification: CELL ADHESION
• Organism(s): Gallus gallus
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2010-06-18 Released: 2010-11-10 
• Deposition Author(s): Monne, M., Jovine, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.249 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.18 kDa 
• Atom Count: 4,695 
• Modelled Residue Count: 589 
• Deposited Residue Count: 654 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida 3	A, B	297	Gallus gallus	Mutation(s): 1
UniProt
Find proteins for P79762 (Gallus gallus) Explore P79762  Go to UniProtKB:  P79762

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida 3	C, D	30	Gallus gallus	Mutation(s): 3
UniProt
Find proteins for P79762 (Gallus gallus) Explore P79762  Go to UniProtKB:  P79762

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	E	2		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G00031MO GlyCosmos:  G00031MO GlyGen:  G00031MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	F [auth C]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084	E	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.249 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.385	α = 90
b = 98.385	β = 90
c = 257.369	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Monne, M., Jovine, L.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary