2R2B

Crystal structure of S25-2 Fab in complex with Kdo analogues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.231

Literature

Macromolecules
Sequence Display for 2R2B

Classification: IMMUNE SYSTEM

Total Structure Weight: 49239.32

Macromolecule Entities
Molecule Chains Length Organism Details
Fab, antibody fragment (IgG1k), light chain A 219 Mus musculus Gene Name(s): Igkv8-30 Gm10883
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fab, antibody fragment (IgG1k), heavy chain B 222 Mus musculus

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

B (3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O- ALLYL
C11 H18 O8
LEEKAQBTVJRLOA-UEWQFTGXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
KDO
Query on KDO

B 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
KDA N/A in BindingDB
N/A in BindingMoad
Kd: 63000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.231
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 45.89 α = 90.00
b = 81.66 β = 90.00
c = 131.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-08-24
  • Released Date: 2008-12-30
  • Deposition author(s): Brooks, C.L., Evans, S.V.

Revision History

  • 2011-07-13
    Type: Version format compliance