1XWV | pdb_00001xwv

Structure of the house dust mite allergen Der f 2: Implications for function and molecular basis of IgE cross-reactivity

PDB DOI: https://doi.org/10.2210/pdb1XWV/pdb

Classification: ALLERGEN
Organism(s): Dermatophagoides farinae
Expression System: Komagataella pastoris
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2004-11-02 Released: 2004-12-14
Deposition Author(s): Johannessen, B.R., Skov, L.K., Kastrup, J.S., Kristensen, O., Bolwig, C., Larsen, J.N., Spangfort, M., Lund, K., Gajhede, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.257 (Depositor), 0.237 (DCC)
R-Value Work:
0.221 (Depositor), 0.228 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity.

Johannessen, B.R., Skov, L.K., Kastrup, J.S., Kristensen, O., Bolwig, C., Larsen, J.N., Spangfort, M., Lund, K., Gajhede, M.

(2005) FEBS Lett 579: 1208-1212

PubMed: 15710415 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2004.11.115
Primary Citation Related Structures:
1XWV

PubMed Abstract:
The X-ray structure of the group 2 major allergen from Dermatophagoides farinae (Der f 2) was determined to 1.83 A resolution. The overall Der f 2 structure comprises a single domain of immunoglobulin fold with two anti-parallel beta-sheets. A large hydrophobic cavity is formed in the interior of Der f 2. Structural comparisons to distantly related proteins suggest a role in lipid binding. Immunoglobulin E (IgE) cross-reactivity between group 2 house dust mite major allergens can be explained by conserved surface areas representing IgE binding epitopes.

Organizational Affiliation

Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 29.2 kDa
Atom Count: 2,329
Modeled Residue Count: 258
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Der f II	A, B	129	Dermatophagoides farinae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q00855 (Dermatophagoides farinae) Explore Q00855 Go to UniProtKB: Q00855
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00855
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
XPE Query on XPE Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.257 (Depositor), 0.237 (DCC)
R-Value Work: 0.221 (Depositor), 0.228 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.712	α = 85.98
b = 47.638	β = 75.9
c = 48.275	γ = 82.76

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-12-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-12-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary