2X57

Crystal structure of the extracellular domain of human Vasoactive intestinal polypeptide receptor 2

• PDB DOI: https://doi.org/10.2210/pdb2X57/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-05 Released: 2010-03-09 
• Deposition Author(s): Pike, A.C.W., Barr, A.J., Quigley, A., Burgess Brown, N., de Riso, A., Bullock, A., Berridge, G., Muniz, J.R.C., Chaikaud, A., Vollmar, M., Krojer, T., Ugochukwu, E., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Carpenter, E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal Structure of the Extracellular Domain of Human Vasoactive Intestinal Polypeptide Receptor 2

Pike, A.C.W., Barr, A.J., Quigley, A., Burgess Brown, N., De Riso, A., Bullock, A., Berridge, G., Muniz, J.R.C., Chaikaud, A., Vollmar, M., Krojer, T., Ugochukwu, E., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Carpenter, E.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.79 kDa 
• Atom Count: 2,579 
• Modelled Residue Count: 311 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2	A, B, C	116	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P41587 (Homo sapiens) Explore P41587  Go to UniProtKB:  P41587
PHAROS:  P41587 GTEx:  ENSG00000106018

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.7	α = 90
b = 99.7	β = 90
c = 104.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Pike, A.C.W., Barr, A.J., Quigley, A., Burgess Brown, N., de Riso, A., Bullock, A., Berridge, G., Muniz, J.R.C., Chaikaud, A., Vollmar, M., Krojer, T., Ugochukwu, E., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Carpenter, E.P.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary