1M7D

Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide

Structural Biology Knowledgebase: 1M7D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 1M7D

Classification: IMMUNE SYSTEM

Total Structure Weight: 47776.55

Macromolecule Entities
Molecule Chains Length Organism Details
light chain of the monoclonal antibody Fab SYA/J6 A 215 Mus musculus Gene Name(s): Igkc Igk-C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
heavy chain of the monoclonal antibody Fab SYA/J6 B 220 Mus musculus Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
C9 H17 N O6
ZEVOCXOZYFLVKN-JGKVKWKGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RAM
Query on RAM

A ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RAE
Query on RAE

A 2-DEOXY-ALPHA-RHAMNOSE
C6 H12 O4
FDWRIIDFYSUTDP-AZGQCCRYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.216
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 71.00 α = 90.00
b = 71.00 β = 90.00
c = 198.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-19
  • Released Date: 2003-07-22
  • Deposition author(s): Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4