1YEI

CATALYTIC ANTIBODY D2.3 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 1YEI

Classification: IMMUNE SYSTEM

Total Structure Weight: 49013.15

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN)) L 219 Mus musculus Fragment: ANTIGEN BINDING DOMAIN
Gene Name(s): Igk
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN)) H 222 Mus musculus Fragment: ANTIGEN BINDING DOMAIN

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

L PARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE
N-PYRIDOXYL-3-[2-AMINO-ETHOXY-METHYLENE]ALANINE- 5-MONOPHOSPHATE (Synonym)
C12 H15 N2 O8 P
WLNKGRQBMNPVSJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PGG N/A in BindingDB
Kd: 35 nM  BindingMOAD
Kd: 35 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.204
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 78.35 α = 90.00
b = 78.35 β = 90.00
c = 159.28 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-08-13
  • Released Date: 1999-01-13
  • Deposition author(s): Gigant, B., Knossow, M.

Revision History

  • Version 1_0: 1999-01-13

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance