2R1X

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: 0.239
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 2R1X

Classification: IMMUNE SYSTEM

Total Structure Weight: 48950.32

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 Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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)
KDD
Query on KDD

A 2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid
5-deoxy-4-epi-2,3-dehydro-alpha-D-manno-oct- 2-ulosonic acid (Synonym)
C8 H12 O6
DVEBLXNKVWKMJU-PBXRRBTRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
KDD N/A in BindingDB
N/A in BindingMoad
Kd: 16000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.217
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 45.94 α = 90.00
b = 81.49 β = 90.00
c = 131.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-08-23
  • Released Date: 2008-12-30
  • Deposition author(s): Brooks, C.L., Evans, S.V.

Revision History

  • 2011-07-13
    Type: Version format compliance