1NDG

Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme

Structural Biology Knowledgebase: 1NDG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NDG

Classification: IMMUNE SYSTEM / HYDROLASE

Total Structure Weight: 60615.67

Macromolecule Entities
Molecule Chains Length Organism Details
antibody kappa light chain A 214 Mus musculus Fragment: light chain
Details: first chain of Anti-Lysozyme Antibody HyHEL-8
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
immunoglobulin gamma 1 chain B 210 Mus musculus Details: second chain of Anti-Lysozyme Antibody HyHEL-8
Gene Name(s): Igh-1a
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Lysozyme C C 129 Gallus gallus EC#: 3.2.1.17 IUBMB
Mutation: R661A
Gene Name(s): LYZ Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.206
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.87 α = 90.00
b = 89.87 β = 90.00
c = 148.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-09
  • Released Date: 2003-06-03
  • Deposition author(s): Mariuzza, R.A., Li, Y., Li, H., Yang, F., Smith-Gill, S.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4