4YO0

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 4YO0

Classification: IMMUNE SYSTEM

Total Structure Weight: 104861.67

Macromolecule Entities
Molecule Chains Length Organism Details
Heavy chain of antigen binding fragment, Fab A, C 238 Rattus norvegicus
Light chain of antigen binding fragment, Fab B, D 233 Rattus norvegicus
PA14 peptide E, F 14 Homo sapiens Gene Name(s): PDPN Gene View GP36 PSEC0003 PSEC0025
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EDO
Query on EDO

D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
B, D L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.179
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 42.18 α = 90.00
b = 80.01 β = 96.61
c = 132.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-03-11
  • Released Date: 2016-03-02
  • Deposition author(s): Fujii, Y., Kitago, Y., Arimori, T., Takagi, J.

Revision History

  • 2016-04-13
    Type: Database references