4ODT

Fab Structure of lipid A-specific antibody S1-15 in complex with lipid A carbohydrate backbone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 4ODT

Classification: IMMUNE SYSTEM

Total Structure Weight: 49075.20

Macromolecule Entities
Molecule Chains Length Organism Details
S1-15 Fab (IgG2b) heavy chain H 226 Mus musculus
S1-15 Fab (IgG2b kappa) light chain L 214 Mus musculus

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GP1
Query on GP1

H GLUCOSAMINE 1-PHOSPHATE
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Z9M
Query on Z9M

H 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-QZABAPFNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG0
Query on PG0

H, L 2-(2-METHOXYETHOXY)ETHANOL
PEG 6000 (Synonym)
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.197
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 77.47 α = 90.00
b = 77.47 β = 90.00
c = 156.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-01-10
  • Released Date: 2015-06-24
  • Deposition author(s): Haji-Ghassemi, O., Evans, S.V.

Revision History

  • Version 1_0: 2015-06-24

    Type: Initial release

  • Version 1_1: 2015-07-01

    Type: Database references

  • Version 1_2: 2015-10-07

    Type: Database references

  • Version 1_3: 2017-11-22

    Type: Refinement description