5X5W

Crystal structure of pseudorabies virus glycoprotein D

• PDB DOI: https://doi.org/10.2210/pdb5X5W/pdb

• Classification: VIRAL PROTEIN/CELL ADHESION
• Organism(s): Suid alphaherpesvirus 1, Sus scrofa
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-02-17 Released: 2017-04-26 
• Deposition Author(s): Li, A., Lu, G., Qi, J., Wu, L., Tian, K., Luo, T., Shi, Y., Yan, J., Gao, G.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Crystal structure of pseudorabies virus glycoprotein D

Li, A., Lu, G., Qi, J., Wu, L., Tian, K., Luo, T., Shi, Y., Yan, J., Gao, G.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.97 kDa 
• Atom Count: 5,542 
• Modelled Residue Count: 680 
• Deposited Residue Count: 1,018 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GD	A, C	402	Suid alphaherpesvirus 1	Mutation(s): 0  Gene Names: US6
UniProt
Find proteins for P07645 (Suid herpesvirus 1 (strain Rice)) Explore P07645  Go to UniProtKB:  P07645

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nectin-1	B, D	107	Sus scrofa	Mutation(s): 0  Gene Names: NECTIN1, HVEC, PRR1, PVRL1
UniProt
Find proteins for Q9GL76 (Sus scrofa) Explore Q9GL76  Go to UniProtKB:  Q9GL76

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.945	α = 90
b = 98.11	β = 90
c = 128.395	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Li, A., Lu, G., Qi, J., Wu, L., Tian, K., Luo, T., Shi, Y., Yan, J., Gao, G.F.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary