8DUZ

Protective antibody against gonococcal lipooligosaccharide bound to peptide mimetic

• PDB DOI: https://doi.org/10.2210/pdb8DUZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Bacteriophage sp.
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-07-27 Released: 2023-07-05 
• Deposition Author(s): Beernink, P.T., Beernink, B.P., Rice, P.A., Ram, S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

Protective antibody against gonococcal lipooligosaccharide bound to peptide mimetic

Beernink, P.T., Beernink, B.P., Ram, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 97.13 kDa 
• Atom Count: 7,172 
• Modelled Residue Count: 865 
• Deposited Residue Count: 906 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG heavy chain, Fd fragment	A, B [auth C]	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig, lambda light chain	C [auth D], D [auth B]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mimetic peptide	E, F	17	Bacteriophage sp.	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth C], J [auth C], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.61	α = 90
b = 64.19	β = 97.12
c = 110.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Beernink, P.T., Beernink, B.P., Rice, P.A., Ram, S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI134868

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description