5DQ9 | pdb_00005dq9

Structure of S55-3 Fab in complex with Lipid A

• PDB DOI: https://doi.org/10.2210/pdb5DQ9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2015-09-14 Released: 2016-03-09 
• Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.245 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from from unrelated V-genes

Haji-Ghassemi, O., Muller-Loennies, S., Rodriguez, T., Brade, L., Kosma, P., Brade, H., Evans, S.V.

(2015) J Biological Chem 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 144.29 kDa 
• Atom Count: 10,397 
• Modeled Residue Count: 1,292 
• Deposited Residue Count: 1,320 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S55-3 Fab (IgG2b) heavy chain	A, C, E [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAb 44B1 light chain	B, D, F [auth L]	218	Mus musculus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose	G [auth E], H [auth F], I [auth G]	2		N/A
Glycosylation Resources
GlyTouCan: G84001BP GlyCosmos: G84001BP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	J [auth C], K [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.245 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 338.121	α = 90
b = 52.865	β = 100.95
c = 75.391	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary