4X1Z

Crystal structure of RHDVb P domain in complex with H type 2

• PDB DOI: https://doi.org/10.2210/pdb4X1Z/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rabbit hemorrhagic disease virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-25 Released: 2015-01-14 
• Deposition Author(s): Leuthold, M.M., Hansman, G.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.132 
• R-Value Work: 0.108 
• R-Value Observed: 0.109 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 69.84 kDa 
• Atom Count: 5,773 
• Modelled Residue Count: 664 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	332	Rabbit hemorrhagic disease virus	Mutation(s): 0  Gene Names: VP1
UniProt
Find proteins for I7FLU3 (Rabbit hemorrhagic disease virus) Explore I7FLU3  Go to UniProtKB:  I7FLU3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G42956UG GlyCosmos:  G42956UG GlyGen:  G42956UG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900125	C, D	H type 2 antigen, alpha anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.132 
• R-Value Work: 0.108 
• R-Value Observed: 0.109 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.17	α = 90
b = 76.21	β = 90
c = 107.68	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Leuthold, M.M., Hansman, G.S.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary