5VPG | pdb_00005vpg

CRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.199 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens.

Chruszcz, M.Pomes, A.Glesner, J.Vailes, L.D.Osinski, T.Porebski, P.J.Majorek, K.A.Heymann, P.W.Platts-Mills, T.A.Minor, W.Chapman, M.D.

(2012) J Biological Chem 287: 7388

  • DOI: https://doi.org/10.1074/jbc.M111.311159
  • Primary Citation Related Structures: 
    3RVT, 3RVU, 5VPG, 5VPH, 5VPL

  • PubMed Abstract: 

    House dust mites produce potent allergens, Der p 1 and Der f 1, that cause allergic sensitization and asthma. Der p 1 and Der f 1 are cysteine proteases that elicit IgE responses in 80% of mite-allergic subjects and have proinflammatory properties. Their antigenic structure is unknown. Here, we present crystal structures of natural Der p 1 and Der f 1 in complex with a monoclonal antibody, 4C1, which binds to a unique cross-reactive epitope on both allergens associated with IgE recognition. The 4C1 epitope is formed by almost identical amino acid sequences and contact residues. Mutations of the contact residues abrogate mAb 4C1 binding and reduce IgE antibody binding. These surface-exposed residues are molecular targets that can be exploited for development of recombinant allergen vaccines.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.

Macromolecule Content 

  • Total Structure Weight: 77.26 kDa 
  • Atom Count: 5,637 
  • Modeled Residue Count: 651 
  • Deposited Residue Count: 689 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Der p 1 allergen222Dermatophagoides pteronyssinusMutation(s): 0 
EC: 3.4.22.65
UniProt
Find proteins for P08176 (Dermatophagoides pteronyssinus)
Explore P08176 
Go to UniProtKB:  P08176
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08176
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB 4C1 - LIGHT CHAINB [auth C]212Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB 4C1 - HEAVY CHAINC [auth D]255Mus musculusMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
J [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth C],
L [auth C],
M [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.199 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.803α = 90
b = 61.764β = 90
c = 223.771γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2022-04-13
    Changes: Database references, Structure summary
  • Version 1.3: 2023-10-04
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary