3WFH

Crystal structure of anti-Prostaglandin E2 Fab fragment PGE2 complex

• PDB DOI: https://doi.org/10.2210/pdb3WFH/pdb

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


• Deposited: 2013-07-19 Released: 2014-07-23 
• Deposition Author(s): Sugahara, M., Ago, H., Saino, H., Miyano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.200 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Crystal structure of anti-Prostaglandin E2 Fab fragment with Prostaglandin E2

Sugahara, M., Ago, H., Saino, H., Miyano, M., Kurahashi, Y., Aoyama, S., Takehira, M., Yutani, K., Yamamoto, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 47.53 kDa 
• Atom Count: 3,906 
• Modelled Residue Count: 427 
• Deposited Residue Count: 433 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb Fab H fragment	A	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb Fab L fragment	B	216	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P2E	C [auth B]	(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid C20 H32 O5 XEYBRNLFEZDVAW-ARSRFYASSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.200 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.26	α = 90
b = 82.53	β = 90
c = 82.74	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Sugahara, M., Ago, H., Saino, H., Miyano, M.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary