4PP1

The crystal structure of Der p 1 allergen complexed with Fab fragment of mAb 5H8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 4PP1

Classification: IMMUNE SYSTEM

Total Structure Weight: 153333.09

Macromolecule Entities
Molecule Chains Length Organism Details
Peptidase 1 A, B 222 Dermatophagoides pteronyssinus EC#: 3.4.22.65 IUBMB
Gene Name(s): DERP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
light chain of Fab fragment of mAb 5H8 C, E 210 Mus musculus
heavy chain of Fab fragment of mAb 5H8 D, F 260 Mus musculus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.219
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 47.74 α = 90.00
b = 73.26 β = 91.09
c = 200.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-02-26
  • Released Date: 2015-04-08
  • Deposition author(s): Osinski, T., Majorek, K.A., Pomes, A., Offermann, L.R., Osinski, S., Glesner, J., Vailes, L.D., Chapman, M.D., Minor, W., Chruszcz, M.

Revision History

  • Version 1_0: 2015-04-08

    Type: Initial release

  • Version 2_0: 2017-08-09

    Type: Advisory, Atomic model, Database references, Polymer sequence, Structure summary

  • Version 2_1: 2017-11-22

    Type: Refinement description