4ZCE

Crystal Structure of the dust mite allergen Der p 23 from Dermatophagoides pteronyssinus

PDB DOI: https://doi.org/10.2210/pdb4ZCE/pdb

Classification: ALLERGEN
Organism(s): Dermatophagoides pteronyssinus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-15 Released: 2015-11-25
Deposition Author(s): Pedersen, L.C., Mueller, G.A., Randall, T.A., Glesner, J., Perera, L., Edwards, L.L., Chapman, M.D., London, R.E., Pomes, A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.190
R-Value Work: 0.164
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

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

Literature

Serological, genomic and structural analyses of the major mite allergen Der p 23.

Mueller, G.A., Randall, T.A., Glesner, J., Pedersen, L.C., Perera, L., Edwards, L.L., DeRose, E.F., Chapman, M.D., London, R.E., Pomes, A.

(2016) Clin Exp Allergy 46: 365-376

PubMed: 26602749 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1111/cea.12680
Primary Citation of Related Structures:
4ZCE

PubMed Abstract:
Der p 23 was recently identified in a European population as a major allergen and potentially a chitin binding protein.

Organizational Affiliation

Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA.

Macromolecule Content

Total Structure Weight: 11.95 kDa
Atom Count: 1,024
Modelled Residue Count: 96
Deposited Residue Count: 100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dust mite allergen	A, B	50	Dermatophagoides pteronyssinus	Mutation(s): 0
UniProt
Find proteins for L7N6F8 (Dermatophagoides pteronyssinus) Explore L7N6F8 Go to UniProtKB: L7N6F8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L7N6F8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.190
R-Value Work: 0.164
R-Value Observed: 0.165
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.283	α = 90
b = 53.519	β = 95.47
c = 40.395	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Z01-ES102885, ZIA-ES102645,R01AI077653

Revision History (Full details and data files)

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2015-12-09
Changes: Database references
Version 1.2: 2016-02-10
Changes: Database references
Version 1.3: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.4: 2019-12-11
Changes: Author supporting evidence