9EXM | pdb_00009exm

Cryogenic APO structures of soluble epoxide hydrolase

• PDB DOI: https://doi.org/10.2210/pdb9EXM/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-04-08 Released: 2025-05-21 
• Deposition Author(s): Dunge, A., Kack, H., Branden, G.
• Funding Organization(s): The Swedish Foundation for Strategic Research, Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.229 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Cryogenic APO structures of soluble Epoxide Hydrolase.

Dunge, A., Kack, H., Branden, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.4 kDa 
• Atom Count: 5,044 
• Modeled Residue Count: 546 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional epoxide hydrolase 2	A	549	Homo sapiens	Mutation(s): 0  Gene Names: EPHX2 EC: 3.1.3.76 (UniProt), 3.3.2.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens) Explore P34913  Go to UniProtKB:  P34913
PHAROS:  P34913 GTEx:  ENSG00000120915

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.229 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.156	α = 90
b = 93.156	β = 90
c = 246.213	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Dunge, A., Kack, H., Branden, G.

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Funding Organization	Location	Grant Number
The Swedish Foundation for Strategic Research	Sweden	ID17-0060
Swedish Research Council	Sweden	2017-06734
Swedish Research Council	Sweden	2021-05662
Swedish Research Council	Sweden	2021-05981

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release