› 5vpg

X-ray diffraction
1.95Å resolution

CRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1

Released:
DOI: 10.2210/pdb5vpg/pdb
PDB entry 5vpg coloured by chain, front view.
PDB entry 5vpg coloured by chain, side view.
PDB entry 5vpg coloured by chain, top view.
Source organisms:
Primary publication:
Molecular determinants for antibody binding on group 1 house dust mite allergens.
Chruszcz M, Pomés A, Glesner J, Vailes LD, Osinski T, Porebski PJ, Majorek KA, Heymann PW, Platts-Mills TA, Minor W, Chapman MD
J Biol Chem 287 7388-98 (2012)
PMID: 22210776

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231382 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Der p 1 allergen Chain: A
Molecule details ›
Chain: A
Length: 222 amino acids
Theoretical weight: 25.01 KDa
Source organism: Dermatophagoides pteronyssinus
UniProt:
  • Canonical: Q3HWZ5 (Residues: 81-302; Coverage: 74%)
Sequence domains: Papain family cysteine protease
Structure domains: Cysteine proteinases
FAB 4C1 - LIGHT CHAIN Chain: C
Molecule details ›
Chain: C
Length: 212 amino acids
Theoretical weight: 23.81 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins
FAB 4C1 - HEAVY CHAIN Chain: D
Molecule details ›
Chain: D
Length: 255 amino acids
Theoretical weight: 27.68 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand CA 1 x CA
Ligand EDO 8 x EDO
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 49.803Å b: 61.764Å c: 223.771Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.156 0.199
Expression system: Mus musculus

Quick links

Citations

14 review citations

Structure of allergens and structure based epitope predictions.
Dall'antonia et al. (2014)
13 more

2 mentions without citation

Conformational selection of allergen-antibody complexes-surface plasticity of paratopes and epitopes.
Fernández-Quintero et al. (2019)
1 more