3V0W

Crystal structure of Fab WN1 222-5 in complex with LPS

Structural Biology Knowledgebase: 3V0W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V0W

Classification: IMMUNE SYSTEM

Total Structure Weight: 49716.50

Macromolecule Entities
Molecule Chains Length Organism Details
WN1 222-5 Fab (IgG2a) light chain L 212 Mus musculus
WN1 222-5 Fab (IgG2a) heavy chain H 219 Mus musculus

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GM0
Query on GM0

H 4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose
C7 H15 O10 P
JDFMKMOMBHLESC-OPTWKVKHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
KDO
Query on KDO

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

H L-GLYCERO-D-MANNO-HEPTOPYRANOSE
C7 H14 O7
BGWQRWREUZVRGI-QQABCQGCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLA
Query on GLA

H ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

H ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PA1
Query on PA1

H 2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

H, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.182
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.85 α = 90.00
b = 101.85 β = 90.00
c = 118.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-08
  • Released Date: 2012-12-05
  • Deposition author(s): Gomery, K., Evans, S.V.

Revision History

  • 2013-01-02
    Type: Citation | Details: Citation update