5VCN

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 5VCN

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: 2017-03-31
  • Released Date: 2017-04-26
  • 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.
  • This entry supercedes:

Revision History

  • Version 1_0: 2017-04-26

    Type: Initial release

  • Version 1_1: 2017-05-03

    Type: Derived calculations

  • Version 1_2: 2017-09-20

    Type: Author supporting evidence, Refinement description